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<h1 class="epydoc">Source Code for <a href="dadi.PhiManip-module.html">Module dadi.PhiManip</a></h1>
<pre class="py-src">
<a name="L1"></a><tt class="py-lineno">  1</tt>  <tt class="py-line"><tt class="py-docstring">"""</tt> </tt>
<a name="L2"></a><tt class="py-lineno">  2</tt>  <tt class="py-line"><tt class="py-docstring">Manipulating population frequency spectra phi. e.g. population splittings and</tt> </tt>
<a name="L3"></a><tt class="py-lineno">  3</tt>  <tt class="py-line"><tt class="py-docstring">admixture</tt> </tt>
<a name="L4"></a><tt class="py-lineno">  4</tt>  <tt class="py-line"><tt class="py-docstring">"""</tt> </tt>
<a name="L5"></a><tt class="py-lineno">  5</tt>  <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">numpy</tt> </tt>
<a name="L6"></a><tt class="py-lineno">  6</tt>  <tt class="py-line"><tt class="py-keyword">from</tt> <tt class="py-name">numpy</tt> <tt class="py-keyword">import</tt> <tt class="py-name">newaxis</tt> <tt class="py-keyword">as</tt> <tt class="py-name">nuax</tt> </tt>
<a name="L7"></a><tt class="py-lineno">  7</tt>  <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">scipy</tt><tt class="py-op">.</tt><tt class="py-name">integrate</tt> </tt>
<a name="L8"></a><tt class="py-lineno">  8</tt>  <tt class="py-line"> </tt>
<a name="L9"></a><tt class="py-lineno">  9</tt>  <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-0" class="py-name" targets="Package dadi=dadi-module.html"><a title="dadi" class="py-name" href="#" onclick="return doclink('link-0', 'dadi', 'link-0');">dadi</a></tt> <tt class="py-keyword">import</tt> <tt id="link-1" class="py-name" targets="Module dadi.Numerics=dadi.Numerics-module.html"><a title="dadi.Numerics" class="py-name" href="#" onclick="return doclink('link-1', 'Numerics', 'link-1');">Numerics</a></tt> </tt>
<a name="L10"></a><tt class="py-lineno"> 10</tt>  <tt class="py-line"> </tt>
<a name="phi_1D"></a><div id="phi_1D-def"><a name="L11"></a><tt class="py-lineno"> 11</tt> <a class="py-toggle" href="#" id="phi_1D-toggle" onclick="return toggle('phi_1D');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="dadi.PhiManip-module.html#phi_1D">phi_1D</a><tt class="py-op">(</tt><tt class="py-param">xx</tt><tt class="py-op">,</tt> <tt class="py-param">nu</tt><tt class="py-op">=</tt><tt class="py-number">1.0</tt><tt class="py-op">,</tt> <tt class="py-param">theta0</tt><tt class="py-op">=</tt><tt class="py-number">1.0</tt><tt class="py-op">,</tt> <tt class="py-param">gamma</tt><tt class="py-op">=</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-param">h</tt><tt class="py-op">=</tt><tt class="py-number">0.5</tt><tt class="py-op">,</tt> <tt class="py-param">theta</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-param">beta</tt><tt class="py-op">=</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="phi_1D-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="phi_1D-expanded"><a name="L12"></a><tt class="py-lineno"> 12</tt>  <tt class="py-line">    <tt class="py-docstring">"""</tt> </tt>
<a name="L13"></a><tt class="py-lineno"> 13</tt>  <tt class="py-line"><tt class="py-docstring">    One-dimensional phi for a constant-sized population with genic selection.</tt> </tt>
<a name="L14"></a><tt class="py-lineno"> 14</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L15"></a><tt class="py-lineno"> 15</tt>  <tt class="py-line"><tt class="py-docstring">    xx: one-dimensional grid of frequencies upon which phi is defined</tt> </tt>
<a name="L16"></a><tt class="py-lineno"> 16</tt>  <tt class="py-line"><tt class="py-docstring">    nu: size of this population, relative to the reference population size Nref.</tt> </tt>
<a name="L17"></a><tt class="py-lineno"> 17</tt>  <tt class="py-line"><tt class="py-docstring">    theta0: scaled mutation rate, equal to 4*Nref * u, where u is the mutation </tt> </tt>
<a name="L18"></a><tt class="py-lineno"> 18</tt>  <tt class="py-line"><tt class="py-docstring">            event rate per generation for the simulated locus and Nref is the </tt> </tt>
<a name="L19"></a><tt class="py-lineno"> 19</tt>  <tt class="py-line"><tt class="py-docstring">            reference population size.</tt> </tt>
<a name="L20"></a><tt class="py-lineno"> 20</tt>  <tt class="py-line"><tt class="py-docstring">    gamma: scaled selection coefficient, equal to 4*Nref * s, where s is the</tt> </tt>
<a name="L21"></a><tt class="py-lineno"> 21</tt>  <tt class="py-line"><tt class="py-docstring">           selective advantage.</tt> </tt>
<a name="L22"></a><tt class="py-lineno"> 22</tt>  <tt class="py-line"><tt class="py-docstring">    h: Dominance coefficient. If A is the selected allele, the aa has fitness 1,</tt> </tt>
<a name="L23"></a><tt class="py-lineno"> 23</tt>  <tt class="py-line"><tt class="py-docstring">       aA has fitness 1+2sh and AA has fitness 1+2s. h = 0.5 corresonds to</tt> </tt>
<a name="L24"></a><tt class="py-lineno"> 24</tt>  <tt class="py-line"><tt class="py-docstring">       genic selection.</tt> </tt>
<a name="L25"></a><tt class="py-lineno"> 25</tt>  <tt class="py-line"><tt class="py-docstring">    theta: deprecated in favor of distinct nu and theta0 arguments, for </tt> </tt>
<a name="L26"></a><tt class="py-lineno"> 26</tt>  <tt class="py-line"><tt class="py-docstring">           consistency with Integration functions.</tt> </tt>
<a name="L27"></a><tt class="py-lineno"> 27</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L28"></a><tt class="py-lineno"> 28</tt>  <tt class="py-line"><tt class="py-docstring">    Returns a new phi array.</tt> </tt>
<a name="L29"></a><tt class="py-lineno"> 29</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="L30"></a><tt class="py-lineno"> 30</tt>  <tt class="py-line"> </tt>
<a name="L31"></a><tt class="py-lineno"> 31</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-name">theta</tt> <tt class="py-keyword">is</tt> <tt class="py-keyword">not</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L32"></a><tt class="py-lineno"> 32</tt>  <tt class="py-line">        <tt class="py-keyword">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">(</tt><tt class="py-string">'The parameter theta has been deprecated in favor of '</tt> </tt>
<a name="L33"></a><tt class="py-lineno"> 33</tt>  <tt class="py-line">                         <tt class="py-string">'parameters nu and theta0, for consistency with the '</tt> </tt>
<a name="L34"></a><tt class="py-lineno"> 34</tt>  <tt class="py-line">                         <tt class="py-string">'Integration functions.'</tt><tt class="py-op">)</tt> </tt>
<a name="L35"></a><tt class="py-lineno"> 35</tt>  <tt class="py-line"> </tt>
<a name="L36"></a><tt class="py-lineno"> 36</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-name">h</tt> <tt class="py-op">==</tt> <tt class="py-number">0.5</tt><tt class="py-op">:</tt> </tt>
<a name="L37"></a><tt class="py-lineno"> 37</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt id="link-2" class="py-name" targets="Function dadi.PhiManip.phi_1D_genic()=dadi.PhiManip-module.html#phi_1D_genic"><a title="dadi.PhiManip.phi_1D_genic" class="py-name" href="#" onclick="return doclink('link-2', 'phi_1D_genic', 'link-2');">phi_1D_genic</a></tt><tt class="py-op">(</tt><tt class="py-name">xx</tt><tt class="py-op">,</tt> <tt class="py-name">nu</tt><tt class="py-op">,</tt> <tt class="py-name">theta0</tt><tt class="py-op">,</tt> <tt class="py-name">gamma</tt><tt class="py-op">,</tt> <tt class="py-name">beta</tt><tt class="py-op">=</tt><tt class="py-name">beta</tt><tt class="py-op">)</tt> </tt>
<a name="L38"></a><tt class="py-lineno"> 38</tt>  <tt class="py-line"> </tt>
<a name="L39"></a><tt class="py-lineno"> 39</tt>  <tt class="py-line">    <tt class="py-comment"># Eqn 1 from Williamson, Fledel-Alon, Bustamante _Genetics_ 168:463 (2004).</tt> </tt>
<a name="L40"></a><tt class="py-lineno"> 40</tt>  <tt class="py-line"> </tt>
<a name="L41"></a><tt class="py-lineno"> 41</tt>  <tt class="py-line">    <tt class="py-comment"># Modified to incorporate fact that for beta != 1, we get a term of </tt> </tt>
<a name="L42"></a><tt class="py-lineno"> 42</tt>  <tt class="py-line">    <tt class="py-comment"># 4*beta/(beta+1)^2 in V. This can be implemented by rescaling gamma</tt> </tt>
<a name="L43"></a><tt class="py-lineno"> 43</tt>  <tt class="py-line">    <tt class="py-comment"># and rescaling the final phi.</tt> </tt>
<a name="L44"></a><tt class="py-lineno"> 44</tt>  <tt class="py-line">    <tt class="py-name">gamma</tt> <tt class="py-op">=</tt> <tt class="py-name">gamma</tt> <tt class="py-op">*</tt> <tt class="py-number">4.</tt><tt class="py-op">*</tt><tt class="py-name">beta</tt><tt class="py-op">/</tt><tt class="py-op">(</tt><tt class="py-name">beta</tt><tt class="py-op">+</tt><tt class="py-number">1.</tt><tt class="py-op">)</tt><tt class="py-op">**</tt><tt class="py-number">2</tt> </tt>
<a name="L45"></a><tt class="py-lineno"> 45</tt>  <tt class="py-line"> </tt>
<a name="L46"></a><tt class="py-lineno"> 46</tt>  <tt class="py-line">    <tt class="py-comment"># First we evaluate the relevant integrals.</tt> </tt>
<a name="L47"></a><tt class="py-lineno"> 47</tt>  <tt class="py-line">    <tt class="py-name">ints</tt> <tt class="py-op">=</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">empty</tt><tt class="py-op">(</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">xx</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L48"></a><tt class="py-lineno"> 48</tt>  <tt class="py-line">    <tt class="py-name">integrand</tt> <tt class="py-op">=</tt> <tt class="py-keyword">lambda</tt> <tt class="py-name">xi</tt><tt class="py-op">:</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">exp</tt><tt class="py-op">(</tt><tt class="py-op">-</tt><tt class="py-number">4</tt><tt class="py-op">*</tt><tt class="py-name">gamma</tt><tt class="py-op">*</tt><tt class="py-name">h</tt><tt class="py-op">*</tt><tt class="py-name">xi</tt> <tt class="py-op">-</tt> <tt class="py-number">2</tt><tt class="py-op">*</tt><tt class="py-name">gamma</tt><tt class="py-op">*</tt><tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">-</tt><tt class="py-number">2</tt><tt class="py-op">*</tt><tt class="py-name">h</tt><tt class="py-op">)</tt><tt class="py-op">*</tt><tt class="py-name">xi</tt><tt class="py-op">**</tt><tt class="py-number">2</tt><tt class="py-op">)</tt> </tt>
<a name="L49"></a><tt class="py-lineno"> 49</tt>  <tt class="py-line">    <tt class="py-name">val</tt><tt class="py-op">,</tt> <tt class="py-name">eps</tt> <tt class="py-op">=</tt> <tt class="py-name">scipy</tt><tt class="py-op">.</tt><tt class="py-name">integrate</tt><tt class="py-op">.</tt><tt class="py-name">quad</tt><tt class="py-op">(</tt><tt class="py-name">integrand</tt><tt class="py-op">,</tt> <tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L50"></a><tt class="py-lineno"> 50</tt>  <tt class="py-line">    <tt class="py-name">int0</tt> <tt class="py-op">=</tt> <tt class="py-name">val</tt> </tt>
<a name="L51"></a><tt class="py-lineno"> 51</tt>  <tt class="py-line">    <tt class="py-keyword">for</tt> <tt class="py-name">ii</tt><tt class="py-op">,</tt><tt class="py-name">q</tt> <tt class="py-keyword">in</tt> <tt class="py-name">enumerate</tt><tt class="py-op">(</tt><tt class="py-name">xx</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L52"></a><tt class="py-lineno"> 52</tt>  <tt class="py-line">        <tt class="py-name">val</tt><tt class="py-op">,</tt> <tt class="py-name">eps</tt> <tt class="py-op">=</tt> <tt class="py-name">scipy</tt><tt class="py-op">.</tt><tt class="py-name">integrate</tt><tt class="py-op">.</tt><tt class="py-name">quad</tt><tt class="py-op">(</tt><tt class="py-name">integrand</tt><tt class="py-op">,</tt> <tt class="py-name">q</tt><tt class="py-op">,</tt> <tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L53"></a><tt class="py-lineno"> 53</tt>  <tt class="py-line">        <tt class="py-name">ints</tt><tt class="py-op">[</tt><tt class="py-name">ii</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">val</tt> </tt>
<a name="L54"></a><tt class="py-lineno"> 54</tt>  <tt class="py-line"> </tt>
<a name="L55"></a><tt class="py-lineno"> 55</tt>  <tt class="py-line">    <tt class="py-name">phi</tt> <tt class="py-op">=</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">exp</tt><tt class="py-op">(</tt><tt class="py-number">4</tt><tt class="py-op">*</tt><tt class="py-name">gamma</tt><tt class="py-op">*</tt><tt class="py-name">h</tt><tt class="py-op">*</tt><tt class="py-name">xx</tt> <tt class="py-op">+</tt> <tt class="py-number">2</tt><tt class="py-op">*</tt><tt class="py-name">gamma</tt><tt class="py-op">*</tt><tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">-</tt><tt class="py-number">2</tt><tt class="py-op">*</tt><tt class="py-name">h</tt><tt class="py-op">)</tt><tt class="py-op">*</tt><tt class="py-name">xx</tt><tt class="py-op">**</tt><tt class="py-number">2</tt><tt class="py-op">)</tt><tt class="py-op">*</tt><tt class="py-name">ints</tt><tt class="py-op">/</tt><tt class="py-name">int0</tt> </tt>
<a name="L56"></a><tt class="py-lineno"> 56</tt>  <tt class="py-line">    <tt class="py-comment"># Protect from division by zero errors</tt> </tt>
<a name="L57"></a><tt class="py-lineno"> 57</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-name">xx</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> <tt class="py-op">==</tt> <tt class="py-number">0</tt> <tt class="py-keyword">and</tt> <tt class="py-name">xx</tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> <tt class="py-op">==</tt> <tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L58"></a><tt class="py-lineno"> 58</tt>  <tt class="py-line">        <tt class="py-name">phi</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">:</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> <tt class="py-op">*=</tt> <tt class="py-number">1.</tt><tt class="py-op">/</tt><tt class="py-op">(</tt><tt class="py-name">xx</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">:</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">*</tt><tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">-</tt><tt class="py-name">xx</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">:</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L59"></a><tt class="py-lineno"> 59</tt>  <tt class="py-line">    <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L60"></a><tt class="py-lineno"> 60</tt>  <tt class="py-line">        <tt class="py-name">phi</tt> <tt class="py-op">*=</tt> <tt class="py-number">1.</tt><tt class="py-op">/</tt><tt class="py-op">(</tt><tt class="py-name">xx</tt><tt class="py-op">*</tt><tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">-</tt><tt class="py-name">xx</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L61"></a><tt class="py-lineno"> 61</tt>  <tt class="py-line"> </tt>
<a name="L62"></a><tt class="py-lineno"> 62</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-name">xx</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> <tt class="py-op">==</tt> <tt class="py-number">0</tt><tt class="py-op">:</tt> </tt>
<a name="L63"></a><tt class="py-lineno"> 63</tt>  <tt class="py-line">        <tt class="py-comment"># Technically, phi diverges at 0. This fixes lets us do numerics</tt> </tt>
<a name="L64"></a><tt class="py-lineno"> 64</tt>  <tt class="py-line">        <tt class="py-comment"># sensibly.</tt> </tt>
<a name="L65"></a><tt class="py-lineno"> 65</tt>  <tt class="py-line">        <tt class="py-name">phi</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">phi</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
<a name="L66"></a><tt class="py-lineno"> 66</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-name">xx</tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> <tt class="py-op">==</tt> <tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L67"></a><tt class="py-lineno"> 67</tt>  <tt class="py-line">        <tt class="py-comment"># I used Mathematica to check that this was the proper limit.</tt> </tt>
<a name="L68"></a><tt class="py-lineno"> 68</tt>  <tt class="py-line">        <tt class="py-name">phi</tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-number">1.</tt><tt class="py-op">/</tt><tt class="py-name">int0</tt> </tt>
<a name="L69"></a><tt class="py-lineno"> 69</tt>  <tt class="py-line">    <tt class="py-keyword">return</tt> <tt class="py-name">phi</tt> <tt class="py-op">*</tt> <tt class="py-name">nu</tt><tt class="py-op">*</tt><tt class="py-name">theta0</tt> <tt class="py-op">*</tt> <tt class="py-number">4.</tt><tt class="py-op">*</tt><tt class="py-name">beta</tt><tt class="py-op">/</tt><tt class="py-op">(</tt><tt class="py-name">beta</tt><tt class="py-op">+</tt><tt class="py-number">1.</tt><tt class="py-op">)</tt><tt class="py-op">**</tt><tt class="py-number">2</tt> </tt>
</div><a name="L70"></a><tt class="py-lineno"> 70</tt>  <tt class="py-line"> </tt>
<a name="phi_1D_genic"></a><div id="phi_1D_genic-def"><a name="L71"></a><tt class="py-lineno"> 71</tt> <a class="py-toggle" href="#" id="phi_1D_genic-toggle" onclick="return toggle('phi_1D_genic');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="dadi.PhiManip-module.html#phi_1D_genic">phi_1D_genic</a><tt class="py-op">(</tt><tt class="py-param">xx</tt><tt class="py-op">,</tt> <tt class="py-param">nu</tt><tt class="py-op">=</tt><tt class="py-number">1.0</tt><tt class="py-op">,</tt> <tt class="py-param">theta0</tt><tt class="py-op">=</tt><tt class="py-number">1.0</tt><tt class="py-op">,</tt> <tt class="py-param">gamma</tt><tt class="py-op">=</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-param">theta</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-param">beta</tt><tt class="py-op">=</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="phi_1D_genic-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="phi_1D_genic-expanded"><a name="L72"></a><tt class="py-lineno"> 72</tt>  <tt class="py-line">    <tt class="py-docstring">"""</tt> </tt>
<a name="L73"></a><tt class="py-lineno"> 73</tt>  <tt class="py-line"><tt class="py-docstring">    One-dimensional phi for a constant-sized population with genic selection.</tt> </tt>
<a name="L74"></a><tt class="py-lineno"> 74</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L75"></a><tt class="py-lineno"> 75</tt>  <tt class="py-line"><tt class="py-docstring">    xx: one-dimensional grid of frequencies upon which phi is defined</tt> </tt>
<a name="L76"></a><tt class="py-lineno"> 76</tt>  <tt class="py-line"><tt class="py-docstring">    nu: size of this population, relative to the reference population size Nref.</tt> </tt>
<a name="L77"></a><tt class="py-lineno"> 77</tt>  <tt class="py-line"><tt class="py-docstring">    theta0: scaled mutation rate, equal to 4*Nref * u, where u is the mutation </tt> </tt>
<a name="L78"></a><tt class="py-lineno"> 78</tt>  <tt class="py-line"><tt class="py-docstring">            event rate per generation for the simulated locus and Nref is the </tt> </tt>
<a name="L79"></a><tt class="py-lineno"> 79</tt>  <tt class="py-line"><tt class="py-docstring">            reference population size.</tt> </tt>
<a name="L80"></a><tt class="py-lineno"> 80</tt>  <tt class="py-line"><tt class="py-docstring">    gamma: scaled selection coefficient, equal to 4*Nc * s, where s is the</tt> </tt>
<a name="L81"></a><tt class="py-lineno"> 81</tt>  <tt class="py-line"><tt class="py-docstring">           selective advantage.</tt> </tt>
<a name="L82"></a><tt class="py-lineno"> 82</tt>  <tt class="py-line"><tt class="py-docstring">    theta: deprecated in favor of distinct nu and theta0 arguments, for </tt> </tt>
<a name="L83"></a><tt class="py-lineno"> 83</tt>  <tt class="py-line"><tt class="py-docstring">           consistency with Integration functions.</tt> </tt>
<a name="L84"></a><tt class="py-lineno"> 84</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L85"></a><tt class="py-lineno"> 85</tt>  <tt class="py-line"><tt class="py-docstring">    Returns a new phi array.</tt> </tt>
<a name="L86"></a><tt class="py-lineno"> 86</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="L87"></a><tt class="py-lineno"> 87</tt>  <tt class="py-line"> </tt>
<a name="L88"></a><tt class="py-lineno"> 88</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-name">theta</tt> <tt class="py-keyword">is</tt> <tt class="py-keyword">not</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L89"></a><tt class="py-lineno"> 89</tt>  <tt class="py-line">        <tt class="py-keyword">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">(</tt><tt class="py-string">'The parameter theta has been deprecated in favor of '</tt> </tt>
<a name="L90"></a><tt class="py-lineno"> 90</tt>  <tt class="py-line">                         <tt class="py-string">'parameters nu and theta0, for consistency with the '</tt> </tt>
<a name="L91"></a><tt class="py-lineno"> 91</tt>  <tt class="py-line">                         <tt class="py-string">'Integration functions.'</tt><tt class="py-op">)</tt> </tt>
<a name="L92"></a><tt class="py-lineno"> 92</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-name">gamma</tt> <tt class="py-op">==</tt> <tt class="py-number">0</tt><tt class="py-op">:</tt> </tt>
<a name="L93"></a><tt class="py-lineno"> 93</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt id="link-3" class="py-name" targets="Function dadi.PhiManip.phi_1D_snm()=dadi.PhiManip-module.html#phi_1D_snm"><a title="dadi.PhiManip.phi_1D_snm" class="py-name" href="#" onclick="return doclink('link-3', 'phi_1D_snm', 'link-3');">phi_1D_snm</a></tt><tt class="py-op">(</tt><tt class="py-name">xx</tt><tt class="py-op">,</tt> <tt class="py-name">nu</tt><tt class="py-op">,</tt> <tt class="py-name">theta0</tt><tt class="py-op">,</tt> <tt class="py-name">beta</tt><tt class="py-op">=</tt><tt class="py-name">beta</tt><tt class="py-op">)</tt> </tt>
<a name="L94"></a><tt class="py-lineno"> 94</tt>  <tt class="py-line"> </tt>
<a name="L95"></a><tt class="py-lineno"> 95</tt>  <tt class="py-line">    <tt class="py-comment"># Beta effectively re-scales gamma.</tt> </tt>
<a name="L96"></a><tt class="py-lineno"> 96</tt>  <tt class="py-line">    <tt class="py-name">gamma</tt> <tt class="py-op">=</tt> <tt class="py-name">gamma</tt> <tt class="py-op">*</tt> <tt class="py-number">4.</tt><tt class="py-op">*</tt><tt class="py-name">beta</tt><tt class="py-op">/</tt><tt class="py-op">(</tt><tt class="py-name">beta</tt><tt class="py-op">+</tt><tt class="py-number">1.</tt><tt class="py-op">)</tt><tt class="py-op">**</tt><tt class="py-number">2</tt> </tt>
<a name="L97"></a><tt class="py-lineno"> 97</tt>  <tt class="py-line"> </tt>
<a name="L98"></a><tt class="py-lineno"> 98</tt>  <tt class="py-line">    <tt class="py-name">exp</tt> <tt class="py-op">=</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">exp</tt> </tt>
<a name="L99"></a><tt class="py-lineno"> 99</tt>  <tt class="py-line">    <tt class="py-comment"># Protect from warnings on divisino by zero</tt> </tt>
<a name="L100"></a><tt class="py-lineno">100</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-name">xx</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> <tt class="py-op">==</tt> <tt class="py-number">0</tt> <tt class="py-keyword">and</tt> <tt class="py-name">xx</tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> <tt class="py-op">==</tt> <tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L101"></a><tt class="py-lineno">101</tt>  <tt class="py-line">        <tt class="py-name">phi</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt><tt class="py-op">*</tt><tt class="py-name">xx</tt> </tt>
<a name="L102"></a><tt class="py-lineno">102</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">gamma</tt> <tt class="py-op">&gt;</tt> <tt class="py-op">-</tt><tt class="py-number">300</tt><tt class="py-op">:</tt> </tt>
<a name="L103"></a><tt class="py-lineno">103</tt>  <tt class="py-line">            <tt class="py-name">phi</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">:</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-number">1.</tt><tt class="py-op">/</tt><tt class="py-op">(</tt><tt class="py-name">xx</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">:</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">*</tt><tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">-</tt><tt class="py-name">xx</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">:</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">)</tt>\ </tt>
<a name="L104"></a><tt class="py-lineno">104</tt>  <tt class="py-line">                    <tt class="py-op">*</tt> <tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">-</tt><tt class="py-name">exp</tt><tt class="py-op">(</tt><tt class="py-op">-</tt><tt class="py-number">2</tt><tt class="py-op">*</tt><tt class="py-name">gamma</tt><tt class="py-op">*</tt><tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">-</tt><tt class="py-name">xx</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">:</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">/</tt><tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">-</tt><tt class="py-name">exp</tt><tt class="py-op">(</tt><tt class="py-op">-</tt><tt class="py-number">2</tt><tt class="py-op">*</tt><tt class="py-name">gamma</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L105"></a><tt class="py-lineno">105</tt>  <tt class="py-line">        <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L106"></a><tt class="py-lineno">106</tt>  <tt class="py-line">            <tt class="py-comment"># Avoid overflow issues for very negative gammas</tt> </tt>
<a name="L107"></a><tt class="py-lineno">107</tt>  <tt class="py-line">            <tt class="py-name">phi</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">:</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-number">1.</tt><tt class="py-op">/</tt><tt class="py-op">(</tt><tt class="py-name">xx</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">:</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">*</tt><tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">-</tt><tt class="py-name">xx</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">:</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> <tt class="py-op">*</tt> <tt class="py-name">exp</tt><tt class="py-op">(</tt><tt class="py-number">2</tt><tt class="py-op">*</tt><tt class="py-name">gamma</tt><tt class="py-op">*</tt><tt class="py-name">xx</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">:</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L108"></a><tt class="py-lineno">108</tt>  <tt class="py-line">    <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L109"></a><tt class="py-lineno">109</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">gamma</tt> <tt class="py-op">&gt;</tt> <tt class="py-op">-</tt><tt class="py-number">300</tt><tt class="py-op">:</tt> </tt>
<a name="L110"></a><tt class="py-lineno">110</tt>  <tt class="py-line">            <tt class="py-name">phi</tt> <tt class="py-op">=</tt> <tt class="py-number">1.</tt><tt class="py-op">/</tt><tt class="py-op">(</tt><tt class="py-name">xx</tt><tt class="py-op">*</tt><tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">-</tt><tt class="py-name">xx</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> <tt class="py-op">*</tt> <tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">-</tt><tt class="py-name">exp</tt><tt class="py-op">(</tt><tt class="py-op">-</tt><tt class="py-number">2</tt><tt class="py-op">*</tt><tt class="py-name">gamma</tt><tt class="py-op">*</tt><tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">-</tt><tt class="py-name">xx</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">/</tt><tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">-</tt><tt class="py-name">exp</tt><tt class="py-op">(</tt><tt class="py-op">-</tt><tt class="py-number">2</tt><tt class="py-op">*</tt><tt class="py-name">gamma</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L111"></a><tt class="py-lineno">111</tt>  <tt class="py-line">        <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L112"></a><tt class="py-lineno">112</tt>  <tt class="py-line">            <tt class="py-name">phi</tt> <tt class="py-op">=</tt> <tt class="py-number">1.</tt><tt class="py-op">/</tt><tt class="py-op">(</tt><tt class="py-name">xx</tt><tt class="py-op">*</tt><tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">-</tt><tt class="py-name">xx</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> <tt class="py-op">*</tt> <tt class="py-name">exp</tt><tt class="py-op">(</tt><tt class="py-number">2</tt><tt class="py-op">*</tt><tt class="py-name">gamma</tt><tt class="py-op">*</tt><tt class="py-name">xx</tt><tt class="py-op">)</tt> </tt>
<a name="L113"></a><tt class="py-lineno">113</tt>  <tt class="py-line"> </tt>
<a name="L114"></a><tt class="py-lineno">114</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-name">xx</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> <tt class="py-op">==</tt> <tt class="py-number">0</tt><tt class="py-op">:</tt> </tt>
<a name="L115"></a><tt class="py-lineno">115</tt>  <tt class="py-line">        <tt class="py-name">phi</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">phi</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
<a name="L116"></a><tt class="py-lineno">116</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-name">xx</tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> <tt class="py-op">==</tt> <tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L117"></a><tt class="py-lineno">117</tt>  <tt class="py-line">        <tt class="py-name">limit</tt> <tt class="py-op">=</tt> <tt class="py-number">2</tt><tt class="py-op">*</tt><tt class="py-name">gamma</tt> <tt class="py-op">*</tt> <tt class="py-name">exp</tt><tt class="py-op">(</tt><tt class="py-number">2</tt><tt class="py-op">*</tt><tt class="py-name">gamma</tt><tt class="py-op">)</tt><tt class="py-op">/</tt><tt class="py-op">(</tt><tt class="py-name">exp</tt><tt class="py-op">(</tt><tt class="py-number">2</tt><tt class="py-op">*</tt><tt class="py-name">gamma</tt><tt class="py-op">)</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L118"></a><tt class="py-lineno">118</tt>  <tt class="py-line">        <tt class="py-name">phi</tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">limit</tt> </tt>
<a name="L119"></a><tt class="py-lineno">119</tt>  <tt class="py-line">    <tt class="py-keyword">return</tt> <tt class="py-name">phi</tt> <tt class="py-op">*</tt> <tt class="py-name">nu</tt><tt class="py-op">*</tt><tt class="py-name">theta0</tt> <tt class="py-op">*</tt> <tt class="py-number">4.</tt><tt class="py-op">*</tt><tt class="py-name">beta</tt><tt class="py-op">/</tt><tt class="py-op">(</tt><tt class="py-name">beta</tt><tt class="py-op">+</tt><tt class="py-number">1.</tt><tt class="py-op">)</tt><tt class="py-op">**</tt><tt class="py-number">2</tt> </tt>
</div><a name="L120"></a><tt class="py-lineno">120</tt>  <tt class="py-line"> </tt>
<a name="phi_1D_snm"></a><div id="phi_1D_snm-def"><a name="L121"></a><tt class="py-lineno">121</tt> <a class="py-toggle" href="#" id="phi_1D_snm-toggle" onclick="return toggle('phi_1D_snm');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="dadi.PhiManip-module.html#phi_1D_snm">phi_1D_snm</a><tt class="py-op">(</tt><tt class="py-param">xx</tt><tt class="py-op">,</tt> <tt class="py-param">nu</tt><tt class="py-op">=</tt><tt class="py-number">1.0</tt><tt class="py-op">,</tt> <tt class="py-param">theta0</tt><tt class="py-op">=</tt><tt class="py-number">1.0</tt><tt class="py-op">,</tt> <tt class="py-param">theta</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-param">beta</tt><tt class="py-op">=</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="phi_1D_snm-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="phi_1D_snm-expanded"><a name="L122"></a><tt class="py-lineno">122</tt>  <tt class="py-line">    <tt class="py-docstring">"""</tt> </tt>
<a name="L123"></a><tt class="py-lineno">123</tt>  <tt class="py-line"><tt class="py-docstring">    Standard neutral one-dimensional probability density.</tt> </tt>
<a name="L124"></a><tt class="py-lineno">124</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L125"></a><tt class="py-lineno">125</tt>  <tt class="py-line"><tt class="py-docstring">    xx: one-dimensional grid of frequencies upon which phi is defined</tt> </tt>
<a name="L126"></a><tt class="py-lineno">126</tt>  <tt class="py-line"><tt class="py-docstring">    nu: size of this population, relative to the reference population size Nref.</tt> </tt>
<a name="L127"></a><tt class="py-lineno">127</tt>  <tt class="py-line"><tt class="py-docstring">    theta0: scaled mutation rate, equal to 4*Nref * u, where u is the mutation </tt> </tt>
<a name="L128"></a><tt class="py-lineno">128</tt>  <tt class="py-line"><tt class="py-docstring">            event rate per generation for the simulated locus and Nref is the </tt> </tt>
<a name="L129"></a><tt class="py-lineno">129</tt>  <tt class="py-line"><tt class="py-docstring">            reference population size.</tt> </tt>
<a name="L130"></a><tt class="py-lineno">130</tt>  <tt class="py-line"><tt class="py-docstring">    theta: deprecated in favor of distinct nu and theta0 arguments, for </tt> </tt>
<a name="L131"></a><tt class="py-lineno">131</tt>  <tt class="py-line"><tt class="py-docstring">           consistency with Integration functions.</tt> </tt>
<a name="L132"></a><tt class="py-lineno">132</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L133"></a><tt class="py-lineno">133</tt>  <tt class="py-line"><tt class="py-docstring">    Returns a new phi array.</tt> </tt>
<a name="L134"></a><tt class="py-lineno">134</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="L135"></a><tt class="py-lineno">135</tt>  <tt class="py-line"> </tt>
<a name="L136"></a><tt class="py-lineno">136</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-name">theta</tt> <tt class="py-keyword">is</tt> <tt class="py-keyword">not</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L137"></a><tt class="py-lineno">137</tt>  <tt class="py-line">        <tt class="py-keyword">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">(</tt><tt class="py-string">'The parameter theta has been deprecated in favor of '</tt> </tt>
<a name="L138"></a><tt class="py-lineno">138</tt>  <tt class="py-line">                         <tt class="py-string">'parameters nu and theta0, for consistency with the '</tt> </tt>
<a name="L139"></a><tt class="py-lineno">139</tt>  <tt class="py-line">                         <tt class="py-string">'Integration functions.'</tt><tt class="py-op">)</tt> </tt>
<a name="L140"></a><tt class="py-lineno">140</tt>  <tt class="py-line">    <tt class="py-comment"># Protect from division by zero errors</tt> </tt>
<a name="L141"></a><tt class="py-lineno">141</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-name">xx</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> <tt class="py-op">==</tt> <tt class="py-number">0</tt><tt class="py-op">:</tt> </tt>
<a name="L142"></a><tt class="py-lineno">142</tt>  <tt class="py-line">        <tt class="py-name">phi</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt><tt class="py-op">*</tt><tt class="py-name">xx</tt> </tt>
<a name="L143"></a><tt class="py-lineno">143</tt>  <tt class="py-line">        <tt class="py-name">phi</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">:</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">nu</tt><tt class="py-op">*</tt><tt class="py-name">theta0</tt><tt class="py-op">/</tt><tt class="py-name">xx</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">:</tt><tt class="py-op">]</tt> </tt>
<a name="L144"></a><tt class="py-lineno">144</tt>  <tt class="py-line">        <tt class="py-name">phi</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">phi</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
<a name="L145"></a><tt class="py-lineno">145</tt>  <tt class="py-line">    <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L146"></a><tt class="py-lineno">146</tt>  <tt class="py-line">        <tt class="py-name">phi</tt> <tt class="py-op">=</tt> <tt class="py-name">nu</tt><tt class="py-op">*</tt><tt class="py-name">theta0</tt><tt class="py-op">/</tt><tt class="py-name">xx</tt> </tt>
<a name="L147"></a><tt class="py-lineno">147</tt>  <tt class="py-line">    <tt class="py-keyword">return</tt> <tt class="py-name">phi</tt> <tt class="py-op">*</tt> <tt class="py-number">4.</tt><tt class="py-op">*</tt><tt class="py-name">beta</tt><tt class="py-op">/</tt><tt class="py-op">(</tt><tt class="py-name">beta</tt><tt class="py-op">+</tt><tt class="py-number">1.</tt><tt class="py-op">)</tt><tt class="py-op">**</tt><tt class="py-number">2</tt> </tt>
</div><a name="L148"></a><tt class="py-lineno">148</tt>  <tt class="py-line"> </tt>
<a name="phi_1D_to_2D"></a><div id="phi_1D_to_2D-def"><a name="L149"></a><tt class="py-lineno">149</tt> <a class="py-toggle" href="#" id="phi_1D_to_2D-toggle" onclick="return toggle('phi_1D_to_2D');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="dadi.PhiManip-module.html#phi_1D_to_2D">phi_1D_to_2D</a><tt class="py-op">(</tt><tt class="py-param">xx</tt><tt class="py-op">,</tt> <tt class="py-param">phi_1D</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="phi_1D_to_2D-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="phi_1D_to_2D-expanded"><a name="L150"></a><tt class="py-lineno">150</tt>  <tt class="py-line">    <tt class="py-docstring">"""</tt> </tt>
<a name="L151"></a><tt class="py-lineno">151</tt>  <tt class="py-line"><tt class="py-docstring">    Implement a one-to-two population split.</tt> </tt>
<a name="L152"></a><tt class="py-lineno">152</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L153"></a><tt class="py-lineno">153</tt>  <tt class="py-line"><tt class="py-docstring">    xx: one-dimensional grid of frequencies upon which phi is defined</tt> </tt>
<a name="L154"></a><tt class="py-lineno">154</tt>  <tt class="py-line"><tt class="py-docstring">    phi1D: initial probability density</tt> </tt>
<a name="L155"></a><tt class="py-lineno">155</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L156"></a><tt class="py-lineno">156</tt>  <tt class="py-line"><tt class="py-docstring">    Returns a new two-dimensional phi array.</tt> </tt>
<a name="L157"></a><tt class="py-lineno">157</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="L158"></a><tt class="py-lineno">158</tt>  <tt class="py-line">    <tt class="py-name">pts</tt> <tt class="py-op">=</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">xx</tt><tt class="py-op">)</tt> </tt>
<a name="L159"></a><tt class="py-lineno">159</tt>  <tt class="py-line">    <tt class="py-name">phi_2D</tt> <tt class="py-op">=</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">zeros</tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-name">pts</tt><tt class="py-op">,</tt> <tt class="py-name">pts</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L160"></a><tt class="py-lineno">160</tt>  <tt class="py-line">    <tt class="py-keyword">for</tt> <tt class="py-name">ii</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">,</tt> <tt class="py-name">pts</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L161"></a><tt class="py-lineno">161</tt>  <tt class="py-line">        <tt class="py-name">phi_2D</tt><tt class="py-op">[</tt><tt class="py-name">ii</tt><tt class="py-op">,</tt><tt class="py-name">ii</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt id="link-4" class="py-name" targets="Function dadi.PhiManip.phi_1D()=dadi.PhiManip-module.html#phi_1D"><a title="dadi.PhiManip.phi_1D" class="py-name" href="#" onclick="return doclink('link-4', 'phi_1D', 'link-4');">phi_1D</a></tt><tt class="py-op">[</tt><tt class="py-name">ii</tt><tt class="py-op">]</tt> <tt class="py-op">*</tt> <tt class="py-number">2</tt><tt class="py-op">/</tt><tt class="py-op">(</tt><tt class="py-name">xx</tt><tt class="py-op">[</tt><tt class="py-name">ii</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">-</tt><tt class="py-name">xx</tt><tt class="py-op">[</tt><tt class="py-name">ii</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L162"></a><tt class="py-lineno">162</tt>  <tt class="py-line">    <tt class="py-keyword">return</tt> <tt class="py-name">phi_2D</tt> </tt>
</div><a name="L163"></a><tt class="py-lineno">163</tt>  <tt class="py-line"> </tt>
<a name="phi_2D_to_3D_split_2"></a><div id="phi_2D_to_3D_split_2-def"><a name="L164"></a><tt class="py-lineno">164</tt> <a class="py-toggle" href="#" id="phi_2D_to_3D_split_2-toggle" onclick="return toggle('phi_2D_to_3D_split_2');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="dadi.PhiManip-module.html#phi_2D_to_3D_split_2">phi_2D_to_3D_split_2</a><tt class="py-op">(</tt><tt class="py-param">xx</tt><tt class="py-op">,</tt> <tt class="py-param">phi_2D</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="phi_2D_to_3D_split_2-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="phi_2D_to_3D_split_2-expanded"><a name="L165"></a><tt class="py-lineno">165</tt>  <tt class="py-line">    <tt class="py-docstring">"""</tt> </tt>
<a name="L166"></a><tt class="py-lineno">166</tt>  <tt class="py-line"><tt class="py-docstring">    Split population 2 into populations 2 and 3.</tt> </tt>
<a name="L167"></a><tt class="py-lineno">167</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L168"></a><tt class="py-lineno">168</tt>  <tt class="py-line"><tt class="py-docstring">    xx: one-dimensional grid of frequencies upon which phi is defined</tt> </tt>
<a name="L169"></a><tt class="py-lineno">169</tt>  <tt class="py-line"><tt class="py-docstring">    phi2D: initial probability density</tt> </tt>
<a name="L170"></a><tt class="py-lineno">170</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L171"></a><tt class="py-lineno">171</tt>  <tt class="py-line"><tt class="py-docstring">    Returns a new three-dimensional phi array.</tt> </tt>
<a name="L172"></a><tt class="py-lineno">172</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="L173"></a><tt class="py-lineno">173</tt>  <tt class="py-line">    <tt class="py-keyword">return</tt> <tt id="link-5" class="py-name" targets="Function dadi.PhiManip.phi_2D_to_3D_admix()=dadi.PhiManip-module.html#phi_2D_to_3D_admix"><a title="dadi.PhiManip.phi_2D_to_3D_admix" class="py-name" href="#" onclick="return doclink('link-5', 'phi_2D_to_3D_admix', 'link-5');">phi_2D_to_3D_admix</a></tt><tt class="py-op">(</tt><tt class="py-name">phi_2D</tt><tt class="py-op">,</tt><tt class="py-number">0</tt><tt class="py-op">,</tt><tt class="py-name">xx</tt><tt class="py-op">,</tt><tt class="py-name">xx</tt><tt class="py-op">,</tt><tt class="py-name">xx</tt><tt class="py-op">)</tt> </tt>
</div><a name="L174"></a><tt class="py-lineno">174</tt>  <tt class="py-line"> </tt>
<a name="phi_2D_to_3D_split_1"></a><div id="phi_2D_to_3D_split_1-def"><a name="L175"></a><tt class="py-lineno">175</tt> <a class="py-toggle" href="#" id="phi_2D_to_3D_split_1-toggle" onclick="return toggle('phi_2D_to_3D_split_1');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="dadi.PhiManip-module.html#phi_2D_to_3D_split_1">phi_2D_to_3D_split_1</a><tt class="py-op">(</tt><tt class="py-param">xx</tt><tt class="py-op">,</tt> <tt class="py-param">phi_2D</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="phi_2D_to_3D_split_1-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="phi_2D_to_3D_split_1-expanded"><a name="L176"></a><tt class="py-lineno">176</tt>  <tt class="py-line">    <tt class="py-docstring">"""</tt> </tt>
<a name="L177"></a><tt class="py-lineno">177</tt>  <tt class="py-line"><tt class="py-docstring">    Split population 1 into populations 1 and 3.</tt> </tt>
<a name="L178"></a><tt class="py-lineno">178</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L179"></a><tt class="py-lineno">179</tt>  <tt class="py-line"><tt class="py-docstring">    xx: one-dimensional grid of frequencies upon which phi is defined</tt> </tt>
<a name="L180"></a><tt class="py-lineno">180</tt>  <tt class="py-line"><tt class="py-docstring">    phi2D: initial probability density</tt> </tt>
<a name="L181"></a><tt class="py-lineno">181</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L182"></a><tt class="py-lineno">182</tt>  <tt class="py-line"><tt class="py-docstring">    Returns a new three-dimensional phi array.</tt> </tt>
<a name="L183"></a><tt class="py-lineno">183</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="L184"></a><tt class="py-lineno">184</tt>  <tt class="py-line">    <tt class="py-keyword">return</tt> <tt id="link-6" class="py-name"><a title="dadi.PhiManip.phi_2D_to_3D_admix" class="py-name" href="#" onclick="return doclink('link-6', 'phi_2D_to_3D_admix', 'link-5');">phi_2D_to_3D_admix</a></tt><tt class="py-op">(</tt><tt class="py-name">phi_2D</tt><tt class="py-op">,</tt><tt class="py-number">1</tt><tt class="py-op">,</tt><tt class="py-name">xx</tt><tt class="py-op">,</tt><tt class="py-name">xx</tt><tt class="py-op">,</tt><tt class="py-name">xx</tt><tt class="py-op">)</tt> </tt>
</div><a name="L185"></a><tt class="py-lineno">185</tt>  <tt class="py-line"> </tt>
<a name="_admixture_intermediates"></a><div id="_admixture_intermediates-def"><a name="L186"></a><tt class="py-lineno">186</tt> <a class="py-toggle" href="#" id="_admixture_intermediates-toggle" onclick="return toggle('_admixture_intermediates');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="dadi.PhiManip-module.html#_admixture_intermediates">_admixture_intermediates</a><tt class="py-op">(</tt><tt class="py-param">phi</tt><tt class="py-op">,</tt> <tt class="py-param">ad_z</tt><tt class="py-op">,</tt> <tt class="py-param">zz</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_admixture_intermediates-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_admixture_intermediates-expanded"><a name="L187"></a><tt class="py-lineno">187</tt>  <tt class="py-line">    <tt class="py-comment"># Find where those z values map to in the zz array.</tt> </tt>
<a name="L188"></a><tt class="py-lineno">188</tt>  <tt class="py-line">    <tt class="py-comment"># Note that zz[upper_z[ii,jj]] &gt;= ad_z[ii,jj]</tt> </tt>
<a name="L189"></a><tt class="py-lineno">189</tt>  <tt class="py-line">    <tt class="py-name">upper_z_index</tt> <tt class="py-op">=</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">searchsorted</tt><tt class="py-op">(</tt><tt class="py-name">zz</tt><tt class="py-op">,</tt> <tt class="py-name">ad_z</tt><tt class="py-op">)</tt> </tt>
<a name="L190"></a><tt class="py-lineno">190</tt>  <tt class="py-line">    <tt class="py-comment"># I occasionally seem to get values &gt; 1 (floating pt error) in ad_z. This</tt> </tt>
<a name="L191"></a><tt class="py-lineno">191</tt>  <tt class="py-line">    <tt class="py-comment"># corrects them.</tt> </tt>
<a name="L192"></a><tt class="py-lineno">192</tt>  <tt class="py-line">    <tt class="py-name">upper_z_index</tt> <tt class="py-op">=</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">minimum</tt><tt class="py-op">(</tt><tt class="py-name">upper_z_index</tt><tt class="py-op">,</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">zz</tt><tt class="py-op">)</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L193"></a><tt class="py-lineno">193</tt>  <tt class="py-line">    <tt class="py-comment"># Also ensure that upper_z_index &gt;= 1, so lower_z_index is never &lt; 0.</tt> </tt>
<a name="L194"></a><tt class="py-lineno">194</tt>  <tt class="py-line">    <tt class="py-name">upper_z_index</tt> <tt class="py-op">=</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">maximum</tt><tt class="py-op">(</tt><tt class="py-name">upper_z_index</tt><tt class="py-op">,</tt> <tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L195"></a><tt class="py-lineno">195</tt>  <tt class="py-line">    <tt class="py-name">lower_z_index</tt> <tt class="py-op">=</tt> <tt class="py-name">upper_z_index</tt> <tt class="py-op">-</tt> <tt class="py-number">1</tt> </tt>
<a name="L196"></a><tt class="py-lineno">196</tt>  <tt class="py-line">    <tt class="py-name">upper_z</tt> <tt class="py-op">=</tt> <tt class="py-name">zz</tt><tt class="py-op">[</tt><tt class="py-name">upper_z_index</tt><tt class="py-op">]</tt> </tt>
<a name="L197"></a><tt class="py-lineno">197</tt>  <tt class="py-line">    <tt class="py-name">lower_z</tt> <tt class="py-op">=</tt> <tt class="py-name">zz</tt><tt class="py-op">[</tt><tt class="py-name">lower_z_index</tt><tt class="py-op">]</tt> </tt>
<a name="L198"></a><tt class="py-lineno">198</tt>  <tt class="py-line">     </tt>
<a name="L199"></a><tt class="py-lineno">199</tt>  <tt class="py-line">    <tt class="py-comment"># These are the spacings between points. To special-case the endpoints, we</tt> </tt>
<a name="L200"></a><tt class="py-lineno">200</tt>  <tt class="py-line">    <tt class="py-comment"># use where to set the appropriate spacings to zero. This turns out to be</tt> </tt>
<a name="L201"></a><tt class="py-lineno">201</tt>  <tt class="py-line">    <tt class="py-comment"># what we want to do for proper normalization via the trapezoid rule.</tt> </tt>
<a name="L202"></a><tt class="py-lineno">202</tt>  <tt class="py-line">    <tt class="py-name">delz0</tt> <tt class="py-op">=</tt> <tt class="py-name">zz</tt><tt class="py-op">[</tt><tt class="py-name">lower_z_index</tt><tt class="py-op">]</tt> <tt class="py-op">-</tt> <tt class="py-name">zz</tt><tt class="py-op">[</tt><tt class="py-name">lower_z_index</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
<a name="L203"></a><tt class="py-lineno">203</tt>  <tt class="py-line">    <tt class="py-name">delz0</tt> <tt class="py-op">=</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">where</tt><tt class="py-op">(</tt><tt class="py-name">lower_z_index</tt> <tt class="py-op">==</tt> <tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-name">delz0</tt><tt class="py-op">)</tt> </tt>
<a name="L204"></a><tt class="py-lineno">204</tt>  <tt class="py-line">     </tt>
<a name="L205"></a><tt class="py-lineno">205</tt>  <tt class="py-line">    <tt class="py-name">delz1</tt> <tt class="py-op">=</tt> <tt class="py-name">zz</tt><tt class="py-op">[</tt><tt class="py-name">upper_z_index</tt><tt class="py-op">]</tt> <tt class="py-op">-</tt> <tt class="py-name">zz</tt><tt class="py-op">[</tt><tt class="py-name">lower_z_index</tt><tt class="py-op">]</tt> </tt>
<a name="L206"></a><tt class="py-lineno">206</tt>  <tt class="py-line">    <tt class="py-name">delz1</tt> <tt class="py-op">=</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">where</tt><tt class="py-op">(</tt><tt class="py-name">upper_z_index</tt> <tt class="py-op">==</tt> <tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-name">delz1</tt><tt class="py-op">)</tt> </tt>
<a name="L207"></a><tt class="py-lineno">207</tt>  <tt class="py-line">     </tt>
<a name="L208"></a><tt class="py-lineno">208</tt>  <tt class="py-line">    <tt class="py-name">delz2</tt> <tt class="py-op">=</tt> <tt class="py-name">zz</tt><tt class="py-op">[</tt><tt class="py-op">(</tt><tt class="py-name">upper_z_index</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">%</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">zz</tt><tt class="py-op">)</tt><tt class="py-op">]</tt> <tt class="py-op">-</tt> <tt class="py-name">zz</tt><tt class="py-op">[</tt><tt class="py-name">upper_z_index</tt><tt class="py-op">]</tt> </tt>
<a name="L209"></a><tt class="py-lineno">209</tt>  <tt class="py-line">    <tt class="py-name">delz2</tt> <tt class="py-op">=</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">where</tt><tt class="py-op">(</tt><tt class="py-name">upper_z_index</tt> <tt class="py-op">==</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">zz</tt><tt class="py-op">)</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">,</tt> <tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-name">delz2</tt><tt class="py-op">)</tt> </tt>
<a name="L210"></a><tt class="py-lineno">210</tt>  <tt class="py-line">     </tt>
<a name="L211"></a><tt class="py-lineno">211</tt>  <tt class="py-line">    <tt class="py-comment"># frac_lower is the fraction that gets assigned to the lower z index</tt> </tt>
<a name="L212"></a><tt class="py-lineno">212</tt>  <tt class="py-line">    <tt class="py-name">frac_lower</tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt class="py-name">upper_z</tt> <tt class="py-op">-</tt> <tt class="py-name">ad_z</tt><tt class="py-op">)</tt><tt class="py-op">/</tt><tt class="py-op">(</tt><tt class="py-name">upper_z</tt> <tt class="py-op">-</tt> <tt class="py-name">lower_z</tt><tt class="py-op">)</tt> </tt>
<a name="L213"></a><tt class="py-lineno">213</tt>  <tt class="py-line">    <tt class="py-comment"># frac_upper is the fraction that gets assigned to the upper z index</tt> </tt>
<a name="L214"></a><tt class="py-lineno">214</tt>  <tt class="py-line">    <tt class="py-name">frac_upper</tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt class="py-name">ad_z</tt><tt class="py-op">-</tt><tt class="py-name">lower_z</tt><tt class="py-op">)</tt><tt class="py-op">/</tt><tt class="py-op">(</tt><tt class="py-name">upper_z</tt> <tt class="py-op">-</tt> <tt class="py-name">lower_z</tt><tt class="py-op">)</tt> </tt>
<a name="L215"></a><tt class="py-lineno">215</tt>  <tt class="py-line">    <tt class="py-comment"># This is the overall normalization for the entry</tt> </tt>
<a name="L216"></a><tt class="py-lineno">216</tt>  <tt class="py-line">    <tt class="py-name">norm</tt> <tt class="py-op">=</tt> <tt class="py-number">2</tt><tt class="py-op">*</tt><tt class="py-name">phi</tt><tt class="py-op">/</tt><tt class="py-op">(</tt><tt class="py-name">frac_lower</tt><tt class="py-op">*</tt><tt class="py-name">delz0</tt> <tt class="py-op">+</tt> <tt class="py-name">delz1</tt> <tt class="py-op">+</tt> <tt class="py-name">frac_upper</tt><tt class="py-op">*</tt><tt class="py-name">delz2</tt><tt class="py-op">)</tt> </tt>
<a name="L217"></a><tt class="py-lineno">217</tt>  <tt class="py-line"> </tt>
<a name="L218"></a><tt class="py-lineno">218</tt>  <tt class="py-line">    <tt class="py-keyword">return</tt> <tt class="py-name">lower_z_index</tt><tt class="py-op">,</tt> <tt class="py-name">upper_z_index</tt><tt class="py-op">,</tt> <tt class="py-name">frac_lower</tt><tt class="py-op">,</tt> <tt class="py-name">frac_upper</tt><tt class="py-op">,</tt> <tt class="py-name">norm</tt> </tt>
</div><a name="L219"></a><tt class="py-lineno">219</tt>  <tt class="py-line"> </tt>
<a name="_two_pop_admixture_intermediates"></a><div id="_two_pop_admixture_intermediates-def"><a name="L220"></a><tt class="py-lineno">220</tt> <a class="py-toggle" href="#" id="_two_pop_admixture_intermediates-toggle" onclick="return toggle('_two_pop_admixture_intermediates');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="dadi.PhiManip-module.html#_two_pop_admixture_intermediates">_two_pop_admixture_intermediates</a><tt class="py-op">(</tt><tt class="py-param">phi_2D</tt><tt class="py-op">,</tt> <tt class="py-param">f</tt><tt class="py-op">,</tt> <tt class="py-param">xx</tt><tt class="py-op">,</tt><tt class="py-param">yy</tt><tt class="py-op">,</tt><tt class="py-param">zz</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_two_pop_admixture_intermediates-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_two_pop_admixture_intermediates-expanded"><a name="L221"></a><tt class="py-lineno">221</tt>  <tt class="py-line">    <tt class="py-docstring">"""</tt> </tt>
<a name="L222"></a><tt class="py-lineno">222</tt>  <tt class="py-line"><tt class="py-docstring">    Intermediate results used when splitting a new population out from a 2D phi.</tt> </tt>
<a name="L223"></a><tt class="py-lineno">223</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="L224"></a><tt class="py-lineno">224</tt>  <tt class="py-line">    <tt class="py-comment"># For each point x,y in phi, this is the corresponding frequency z that SNPs</tt> </tt>
<a name="L225"></a><tt class="py-lineno">225</tt>  <tt class="py-line">    <tt class="py-comment"># with frequency x and y in populations 1 and 2 would map to.</tt> </tt>
<a name="L226"></a><tt class="py-lineno">226</tt>  <tt class="py-line">    <tt class="py-name">ad_z</tt> <tt class="py-op">=</tt> <tt class="py-name">f</tt><tt class="py-op">*</tt><tt class="py-name">xx</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-op">,</tt><tt class="py-name">nuax</tt><tt class="py-op">]</tt> <tt class="py-op">+</tt> <tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">-</tt><tt class="py-name">f</tt><tt class="py-op">)</tt><tt class="py-op">*</tt><tt class="py-name">yy</tt><tt class="py-op">[</tt><tt class="py-name">nuax</tt><tt class="py-op">,</tt><tt class="py-op">:</tt><tt class="py-op">]</tt> </tt>
<a name="L227"></a><tt class="py-lineno">227</tt>  <tt class="py-line"> </tt>
<a name="L228"></a><tt class="py-lineno">228</tt>  <tt class="py-line">    <tt class="py-name">lower_z_index</tt><tt class="py-op">,</tt> <tt class="py-name">upper_z_index</tt><tt class="py-op">,</tt> <tt class="py-name">frac_lower</tt><tt class="py-op">,</tt> <tt class="py-name">frac_upper</tt><tt class="py-op">,</tt> <tt class="py-name">norm</tt> \ </tt>
<a name="L229"></a><tt class="py-lineno">229</tt>  <tt class="py-line">            <tt class="py-op">=</tt> <tt id="link-7" class="py-name" targets="Function dadi.PhiManip._admixture_intermediates()=dadi.PhiManip-module.html#_admixture_intermediates"><a title="dadi.PhiManip._admixture_intermediates" class="py-name" href="#" onclick="return doclink('link-7', '_admixture_intermediates', 'link-7');">_admixture_intermediates</a></tt><tt class="py-op">(</tt><tt class="py-name">phi_2D</tt><tt class="py-op">,</tt> <tt class="py-name">ad_z</tt><tt class="py-op">,</tt> <tt class="py-name">zz</tt><tt class="py-op">)</tt> </tt>
<a name="L230"></a><tt class="py-lineno">230</tt>  <tt class="py-line"> </tt>
<a name="L231"></a><tt class="py-lineno">231</tt>  <tt class="py-line">    <tt class="py-keyword">return</tt> <tt class="py-name">lower_z_index</tt><tt class="py-op">,</tt> <tt class="py-name">upper_z_index</tt><tt class="py-op">,</tt> <tt class="py-name">frac_lower</tt><tt class="py-op">,</tt> <tt class="py-name">frac_upper</tt><tt class="py-op">,</tt> <tt class="py-name">norm</tt> </tt>
</div><a name="L232"></a><tt class="py-lineno">232</tt>  <tt class="py-line"> </tt>
<a name="_three_pop_admixture_intermediates"></a><div id="_three_pop_admixture_intermediates-def"><a name="L233"></a><tt class="py-lineno">233</tt> <a class="py-toggle" href="#" id="_three_pop_admixture_intermediates-toggle" onclick="return toggle('_three_pop_admixture_intermediates');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="dadi.PhiManip-module.html#_three_pop_admixture_intermediates">_three_pop_admixture_intermediates</a><tt class="py-op">(</tt><tt class="py-param">phi_3D</tt><tt class="py-op">,</tt> <tt class="py-param">f1</tt><tt class="py-op">,</tt><tt class="py-param">f2</tt><tt class="py-op">,</tt> <tt class="py-param">xx</tt><tt class="py-op">,</tt><tt class="py-param">yy</tt><tt class="py-op">,</tt><tt class="py-param">zz</tt><tt class="py-op">,</tt><tt class="py-param">ww</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_three_pop_admixture_intermediates-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_three_pop_admixture_intermediates-expanded"><a name="L234"></a><tt class="py-lineno">234</tt>  <tt class="py-line">    <tt class="py-docstring">"""</tt> </tt>
<a name="L235"></a><tt class="py-lineno">235</tt>  <tt class="py-line"><tt class="py-docstring">    Intermediate results used when splitting a new population out from a 3D phi.</tt> </tt>
<a name="L236"></a><tt class="py-lineno">236</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L237"></a><tt class="py-lineno">237</tt>  <tt class="py-line"><tt class="py-docstring">    ww: frequency mapping for the new population.</tt> </tt>
<a name="L238"></a><tt class="py-lineno">238</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="L239"></a><tt class="py-lineno">239</tt>  <tt class="py-line">    <tt class="py-comment"># For each point x,y,z in phi, this is the corresponding frequency w that</tt> </tt>
<a name="L240"></a><tt class="py-lineno">240</tt>  <tt class="py-line">    <tt class="py-comment"># SNPs with frequency x,y,z in populations 1,2,3 would map to.</tt> </tt>
<a name="L241"></a><tt class="py-lineno">241</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-name">f1</tt> <tt class="py-op">+</tt> <tt class="py-name">f2</tt> <tt class="py-op">&gt;</tt> <tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L242"></a><tt class="py-lineno">242</tt>  <tt class="py-line">        <tt class="py-keyword">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">(</tt><tt class="py-string">'Admixture proportions (f1=%f, f2 = %f) are '</tt> </tt>
<a name="L243"></a><tt class="py-lineno">243</tt>  <tt class="py-line">                         <tt class="py-string">'non-sensible.'</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt class="py-name">f1</tt><tt class="py-op">,</tt> <tt class="py-name">f2</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L244"></a><tt class="py-lineno">244</tt>  <tt class="py-line">    <tt class="py-name">ad_w</tt> <tt class="py-op">=</tt> <tt class="py-name">f1</tt><tt class="py-op">*</tt><tt class="py-name">xx</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-op">,</tt><tt class="py-name">nuax</tt><tt class="py-op">,</tt><tt class="py-name">nuax</tt><tt class="py-op">]</tt> <tt class="py-op">+</tt> <tt class="py-name">f2</tt><tt class="py-op">*</tt><tt class="py-name">yy</tt><tt class="py-op">[</tt><tt class="py-name">nuax</tt><tt class="py-op">,</tt><tt class="py-op">:</tt><tt class="py-op">,</tt><tt class="py-name">nuax</tt><tt class="py-op">]</tt> <tt class="py-op">+</tt> <tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">-</tt><tt class="py-name">f1</tt><tt class="py-op">-</tt><tt class="py-name">f2</tt><tt class="py-op">)</tt><tt class="py-op">*</tt><tt class="py-name">zz</tt><tt class="py-op">[</tt><tt class="py-name">nuax</tt><tt class="py-op">,</tt><tt class="py-name">nuax</tt><tt class="py-op">,</tt><tt class="py-op">:</tt><tt class="py-op">]</tt> </tt>
<a name="L245"></a><tt class="py-lineno">245</tt>  <tt class="py-line"> </tt>
<a name="L246"></a><tt class="py-lineno">246</tt>  <tt class="py-line">    <tt class="py-name">lower_w_index</tt><tt class="py-op">,</tt> <tt class="py-name">upper_w_index</tt><tt class="py-op">,</tt> <tt class="py-name">frac_lower</tt><tt class="py-op">,</tt> <tt class="py-name">frac_upper</tt><tt class="py-op">,</tt> <tt class="py-name">norm</tt> \ </tt>
<a name="L247"></a><tt class="py-lineno">247</tt>  <tt class="py-line">            <tt class="py-op">=</tt> <tt id="link-8" class="py-name"><a title="dadi.PhiManip._admixture_intermediates" class="py-name" href="#" onclick="return doclink('link-8', '_admixture_intermediates', 'link-7');">_admixture_intermediates</a></tt><tt class="py-op">(</tt><tt class="py-name">phi_3D</tt><tt class="py-op">,</tt> <tt class="py-name">ad_w</tt><tt class="py-op">,</tt> <tt class="py-name">ww</tt><tt class="py-op">)</tt> </tt>
<a name="L248"></a><tt class="py-lineno">248</tt>  <tt class="py-line"> </tt>
<a name="L249"></a><tt class="py-lineno">249</tt>  <tt class="py-line">    <tt class="py-keyword">return</tt> <tt class="py-name">lower_w_index</tt><tt class="py-op">,</tt> <tt class="py-name">upper_w_index</tt><tt class="py-op">,</tt> <tt class="py-name">frac_lower</tt><tt class="py-op">,</tt> <tt class="py-name">frac_upper</tt><tt class="py-op">,</tt> <tt class="py-name">norm</tt> </tt>
</div><a name="L250"></a><tt class="py-lineno">250</tt>  <tt class="py-line"> </tt>
<a name="phi_2D_to_3D_admix"></a><div id="phi_2D_to_3D_admix-def"><a name="L251"></a><tt class="py-lineno">251</tt> <a class="py-toggle" href="#" id="phi_2D_to_3D_admix-toggle" onclick="return toggle('phi_2D_to_3D_admix');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="dadi.PhiManip-module.html#phi_2D_to_3D_admix">phi_2D_to_3D_admix</a><tt class="py-op">(</tt><tt class="py-param">phi</tt><tt class="py-op">,</tt> <tt class="py-param">f</tt><tt class="py-op">,</tt> <tt class="py-param">xx</tt><tt class="py-op">,</tt><tt class="py-param">yy</tt><tt class="py-op">,</tt><tt class="py-param">zz</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="phi_2D_to_3D_admix-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="phi_2D_to_3D_admix-expanded"><a name="L252"></a><tt class="py-lineno">252</tt>  <tt class="py-line">    <tt class="py-docstring">"""</tt> </tt>
<a name="L253"></a><tt class="py-lineno">253</tt>  <tt class="py-line"><tt class="py-docstring">    Create population 3 admixed from populations 1 and 2.</tt> </tt>
<a name="L254"></a><tt class="py-lineno">254</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L255"></a><tt class="py-lineno">255</tt>  <tt class="py-line"><tt class="py-docstring">    Returns a 3D sfs of shape (len(xx),len(yy),len(zz))</tt> </tt>
<a name="L256"></a><tt class="py-lineno">256</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L257"></a><tt class="py-lineno">257</tt>  <tt class="py-line"><tt class="py-docstring">    phi:   phi corresponding to original 2 populations</tt> </tt>
<a name="L258"></a><tt class="py-lineno">258</tt>  <tt class="py-line"><tt class="py-docstring">    f:     Fraction of population 3 derived from population 1. (A fraction 1-f</tt> </tt>
<a name="L259"></a><tt class="py-lineno">259</tt>  <tt class="py-line"><tt class="py-docstring">             will be derived from population 2.)</tt> </tt>
<a name="L260"></a><tt class="py-lineno">260</tt>  <tt class="py-line"><tt class="py-docstring">    xx,yy: Mapping of points in phi to frequencies in populations 1 and 2.</tt> </tt>
<a name="L261"></a><tt class="py-lineno">261</tt>  <tt class="py-line"><tt class="py-docstring">    zz:    Frequency mapping that will be used along population 3 axis.</tt> </tt>
<a name="L262"></a><tt class="py-lineno">262</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="L263"></a><tt class="py-lineno">263</tt>  <tt class="py-line">    <tt class="py-name">lower_z_index</tt><tt class="py-op">,</tt> <tt class="py-name">upper_z_index</tt><tt class="py-op">,</tt> <tt class="py-name">frac_lower</tt><tt class="py-op">,</tt> <tt class="py-name">frac_upper</tt><tt class="py-op">,</tt> <tt class="py-name">norm</tt> \ </tt>
<a name="L264"></a><tt class="py-lineno">264</tt>  <tt class="py-line">            <tt class="py-op">=</tt> <tt id="link-9" class="py-name" targets="Function dadi.PhiManip._two_pop_admixture_intermediates()=dadi.PhiManip-module.html#_two_pop_admixture_intermediates"><a title="dadi.PhiManip._two_pop_admixture_intermediates" class="py-name" href="#" onclick="return doclink('link-9', '_two_pop_admixture_intermediates', 'link-9');">_two_pop_admixture_intermediates</a></tt><tt class="py-op">(</tt><tt class="py-name">phi</tt><tt class="py-op">,</tt> <tt class="py-name">f</tt><tt class="py-op">,</tt> <tt class="py-name">xx</tt><tt class="py-op">,</tt><tt class="py-name">yy</tt><tt class="py-op">,</tt><tt class="py-name">zz</tt><tt class="py-op">)</tt> </tt>
<a name="L265"></a><tt class="py-lineno">265</tt>  <tt class="py-line"> </tt>
<a name="L266"></a><tt class="py-lineno">266</tt>  <tt class="py-line"> </tt>
<a name="L267"></a><tt class="py-lineno">267</tt>  <tt class="py-line">    <tt class="py-comment"># Assemble our result.</tt> </tt>
<a name="L268"></a><tt class="py-lineno">268</tt>  <tt class="py-line">    <tt class="py-comment"># This uses numpy's fancy indexing. It is much, much faster than an</tt> </tt>
<a name="L269"></a><tt class="py-lineno">269</tt>  <tt class="py-line">    <tt class="py-comment"># explicit loop.</tt> </tt>
<a name="L270"></a><tt class="py-lineno">270</tt>  <tt class="py-line">    <tt class="py-comment"># See the numpy-discussion post "Numpy Advanced Indexing Question" by</tt> </tt>
<a name="L271"></a><tt class="py-lineno">271</tt>  <tt class="py-line">    <tt class="py-comment"># Robert Kern on July 16, 2008</tt> </tt>
<a name="L272"></a><tt class="py-lineno">272</tt>  <tt class="py-line">    <tt class="py-comment"># http://projects.scipy.org/pipermail/numpy-discussion/2008-July/035776.html</tt> </tt>
<a name="L273"></a><tt class="py-lineno">273</tt>  <tt class="py-line">    <tt class="py-name">idx_i</tt> <tt class="py-op">=</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">arange</tt><tt class="py-op">(</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">xx</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-op">,</tt><tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">newaxis</tt><tt class="py-op">]</tt> </tt>
<a name="L274"></a><tt class="py-lineno">274</tt>  <tt class="py-line">    <tt class="py-name">idx_j</tt> <tt class="py-op">=</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">arange</tt><tt class="py-op">(</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">yy</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">[</tt><tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">newaxis</tt><tt class="py-op">,</tt><tt class="py-op">:</tt><tt class="py-op">]</tt> </tt>
<a name="L275"></a><tt class="py-lineno">275</tt>  <tt class="py-line"> </tt>
<a name="L276"></a><tt class="py-lineno">276</tt>  <tt class="py-line">    <tt class="py-name">phi_3D</tt> <tt class="py-op">=</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">zeros</tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">xx</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">yy</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">zz</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L277"></a><tt class="py-lineno">277</tt>  <tt class="py-line">    <tt class="py-name">phi_3D</tt><tt class="py-op">[</tt><tt class="py-name">idx_i</tt><tt class="py-op">,</tt> <tt class="py-name">idx_j</tt><tt class="py-op">,</tt> <tt class="py-name">lower_z_index</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">frac_lower</tt><tt class="py-op">*</tt><tt class="py-name">norm</tt> </tt>
<a name="L278"></a><tt class="py-lineno">278</tt>  <tt class="py-line">    <tt class="py-name">phi_3D</tt><tt class="py-op">[</tt><tt class="py-name">idx_i</tt><tt class="py-op">,</tt> <tt class="py-name">idx_j</tt><tt class="py-op">,</tt> <tt class="py-name">upper_z_index</tt><tt class="py-op">]</tt> <tt class="py-op">+=</tt> <tt class="py-name">frac_upper</tt><tt class="py-op">*</tt><tt class="py-name">norm</tt> </tt>
<a name="L279"></a><tt class="py-lineno">279</tt>  <tt class="py-line"> </tt>
<a name="L280"></a><tt class="py-lineno">280</tt>  <tt class="py-line">    <tt class="py-keyword">return</tt> <tt class="py-name">phi_3D</tt> </tt>
</div><a name="L281"></a><tt class="py-lineno">281</tt>  <tt class="py-line"> </tt>
<a name="phi_2D_admix_1_into_2"></a><div id="phi_2D_admix_1_into_2-def"><a name="L282"></a><tt class="py-lineno">282</tt> <a class="py-toggle" href="#" id="phi_2D_admix_1_into_2-toggle" onclick="return toggle('phi_2D_admix_1_into_2');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="dadi.PhiManip-module.html#phi_2D_admix_1_into_2">phi_2D_admix_1_into_2</a><tt class="py-op">(</tt><tt class="py-param">phi</tt><tt class="py-op">,</tt> <tt class="py-param">f</tt><tt class="py-op">,</tt> <tt class="py-param">xx</tt><tt class="py-op">,</tt><tt class="py-param">yy</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="phi_2D_admix_1_into_2-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="phi_2D_admix_1_into_2-expanded"><a name="L283"></a><tt class="py-lineno">283</tt>  <tt class="py-line">    <tt class="py-docstring">"""</tt> </tt>
<a name="L284"></a><tt class="py-lineno">284</tt>  <tt class="py-line"><tt class="py-docstring">    Admix population 1 into population 2.</tt> </tt>
<a name="L285"></a><tt class="py-lineno">285</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L286"></a><tt class="py-lineno">286</tt>  <tt class="py-line"><tt class="py-docstring">    Alters phi in place and returns the new version.</tt> </tt>
<a name="L287"></a><tt class="py-lineno">287</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L288"></a><tt class="py-lineno">288</tt>  <tt class="py-line"><tt class="py-docstring">    phi:   phi corresponding to original 2 populations</tt> </tt>
<a name="L289"></a><tt class="py-lineno">289</tt>  <tt class="py-line"><tt class="py-docstring">    f:     Fraction of updated population 2 to be derived from population 1. </tt> </tt>
<a name="L290"></a><tt class="py-lineno">290</tt>  <tt class="py-line"><tt class="py-docstring">             (A fraction 1-f will be derived from the original population 2.)</tt> </tt>
<a name="L291"></a><tt class="py-lineno">291</tt>  <tt class="py-line"><tt class="py-docstring">    xx,yy: Mapping of points in phi to frequencies in populations 1 and 2.</tt> </tt>
<a name="L292"></a><tt class="py-lineno">292</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="L293"></a><tt class="py-lineno">293</tt>  <tt class="py-line">    <tt class="py-comment"># This is just like the the split_admix situation, but we're splitting into</tt> </tt>
<a name="L294"></a><tt class="py-lineno">294</tt>  <tt class="py-line">    <tt class="py-comment"># a population with zz=yy. We could do this by creating a xx by yy by yy</tt> </tt>
<a name="L295"></a><tt class="py-lineno">295</tt>  <tt class="py-line">    <tt class="py-comment"># array, then integrating out the second population. That's a big waste of</tt> </tt>
<a name="L296"></a><tt class="py-lineno">296</tt>  <tt class="py-line">    <tt class="py-comment"># memory, however.</tt> </tt>
<a name="L297"></a><tt class="py-lineno">297</tt>  <tt class="py-line">    <tt class="py-name">lower_z_index</tt><tt class="py-op">,</tt> <tt class="py-name">upper_z_index</tt><tt class="py-op">,</tt> <tt class="py-name">frac_lower</tt><tt class="py-op">,</tt> <tt class="py-name">frac_upper</tt><tt class="py-op">,</tt> <tt class="py-name">norm</tt> \ </tt>
<a name="L298"></a><tt class="py-lineno">298</tt>  <tt class="py-line">            <tt class="py-op">=</tt> <tt id="link-10" class="py-name"><a title="dadi.PhiManip._two_pop_admixture_intermediates" class="py-name" href="#" onclick="return doclink('link-10', '_two_pop_admixture_intermediates', 'link-9');">_two_pop_admixture_intermediates</a></tt><tt class="py-op">(</tt><tt class="py-name">phi</tt><tt class="py-op">,</tt> <tt class="py-name">f</tt><tt class="py-op">,</tt> <tt class="py-name">xx</tt><tt class="py-op">,</tt><tt class="py-name">yy</tt><tt class="py-op">,</tt><tt class="py-name">yy</tt><tt class="py-op">)</tt> </tt>
<a name="L299"></a><tt class="py-lineno">299</tt>  <tt class="py-line"> </tt>
<a name="L300"></a><tt class="py-lineno">300</tt>  <tt class="py-line">    <tt class="py-comment"># Basically, we're splitting into a third zz population, then integrating</tt> </tt>
<a name="L301"></a><tt class="py-lineno">301</tt>  <tt class="py-line">    <tt class="py-comment"># over yy to be left with the two populations we care about.</tt> </tt>
<a name="L302"></a><tt class="py-lineno">302</tt>  <tt class="py-line">    <tt class="py-name">lower_cont</tt> <tt class="py-op">=</tt> <tt class="py-name">frac_lower</tt><tt class="py-op">*</tt><tt class="py-name">norm</tt> </tt>
<a name="L303"></a><tt class="py-lineno">303</tt>  <tt class="py-line">    <tt class="py-name">upper_cont</tt> <tt class="py-op">=</tt> <tt class="py-name">frac_upper</tt><tt class="py-op">*</tt><tt class="py-name">norm</tt> </tt>
<a name="L304"></a><tt class="py-lineno">304</tt>  <tt class="py-line">    <tt class="py-name">idx_j</tt> <tt class="py-op">=</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">arange</tt><tt class="py-op">(</tt><tt class="py-name">phi</tt><tt class="py-op">.</tt><tt class="py-name">shape</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L305"></a><tt class="py-lineno">305</tt>  <tt class="py-line">    <tt class="py-keyword">for</tt> <tt class="py-name">ii</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-name">phi</tt><tt class="py-op">.</tt><tt class="py-name">shape</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L306"></a><tt class="py-lineno">306</tt>  <tt class="py-line">        <tt class="py-name">phi_int</tt> <tt class="py-op">=</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">zeros</tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-name">phi</tt><tt class="py-op">.</tt><tt class="py-name">shape</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">phi</tt><tt class="py-op">.</tt><tt class="py-name">shape</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L307"></a><tt class="py-lineno">307</tt>  <tt class="py-line">        <tt class="py-comment"># Use fancy indexing to avoid the commented out loop.</tt> </tt>
<a name="L308"></a><tt class="py-lineno">308</tt>  <tt class="py-line">        <tt class="py-comment">#for jj in xrange(len(yy)):</tt> </tt>
<a name="L309"></a><tt class="py-lineno">309</tt>  <tt class="py-line">        <tt class="py-comment">#    phi_int[jj, upper_z_index[ii,jj]] += frac_upper[ii,jj]*norm[ii,jj]</tt> </tt>
<a name="L310"></a><tt class="py-lineno">310</tt>  <tt class="py-line">        <tt class="py-comment">#    phi_int[jj, lower_z_index[ii,jj]] += frac_lower[ii,jj]*norm[ii,jj]</tt> </tt>
<a name="L311"></a><tt class="py-lineno">311</tt>  <tt class="py-line">        <tt class="py-name">phi_int</tt><tt class="py-op">[</tt><tt class="py-name">idx_j</tt><tt class="py-op">,</tt> <tt class="py-name">lower_z_index</tt><tt class="py-op">[</tt><tt class="py-name">ii</tt><tt class="py-op">]</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">lower_cont</tt><tt class="py-op">[</tt><tt class="py-name">ii</tt><tt class="py-op">]</tt> </tt>
<a name="L312"></a><tt class="py-lineno">312</tt>  <tt class="py-line">        <tt class="py-name">phi_int</tt><tt class="py-op">[</tt><tt class="py-name">idx_j</tt><tt class="py-op">,</tt> <tt class="py-name">upper_z_index</tt><tt class="py-op">[</tt><tt class="py-name">ii</tt><tt class="py-op">]</tt><tt class="py-op">]</tt> <tt class="py-op">+=</tt> <tt class="py-name">upper_cont</tt><tt class="py-op">[</tt><tt class="py-name">ii</tt><tt class="py-op">]</tt> </tt>
<a name="L313"></a><tt class="py-lineno">313</tt>  <tt class="py-line">        <tt class="py-name">phi</tt><tt class="py-op">[</tt><tt class="py-name">ii</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt id="link-11" class="py-name"><a title="dadi.Numerics" class="py-name" href="#" onclick="return doclink('link-11', 'Numerics', 'link-1');">Numerics</a></tt><tt class="py-op">.</tt><tt id="link-12" class="py-name" targets="Function dadi.Numerics.trapz()=dadi.Numerics-module.html#trapz"><a title="dadi.Numerics.trapz" class="py-name" href="#" onclick="return doclink('link-12', 'trapz', 'link-12');">trapz</a></tt><tt class="py-op">(</tt><tt class="py-name">phi_int</tt><tt class="py-op">,</tt> <tt class="py-name">yy</tt><tt class="py-op">,</tt> <tt class="py-name">axis</tt><tt class="py-op">=</tt><tt class="py-number">0</tt><tt class="py-op">)</tt> </tt>
<a name="L314"></a><tt class="py-lineno">314</tt>  <tt class="py-line"> </tt>
<a name="L315"></a><tt class="py-lineno">315</tt>  <tt class="py-line">    <tt class="py-keyword">return</tt> <tt class="py-name">phi</tt> </tt>
</div><a name="L316"></a><tt class="py-lineno">316</tt>  <tt class="py-line"> </tt>
<a name="phi_2D_admix_2_into_1"></a><div id="phi_2D_admix_2_into_1-def"><a name="L317"></a><tt class="py-lineno">317</tt> <a class="py-toggle" href="#" id="phi_2D_admix_2_into_1-toggle" onclick="return toggle('phi_2D_admix_2_into_1');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="dadi.PhiManip-module.html#phi_2D_admix_2_into_1">phi_2D_admix_2_into_1</a><tt class="py-op">(</tt><tt class="py-param">phi</tt><tt class="py-op">,</tt> <tt class="py-param">f</tt><tt class="py-op">,</tt> <tt class="py-param">xx</tt><tt class="py-op">,</tt><tt class="py-param">yy</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="phi_2D_admix_2_into_1-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="phi_2D_admix_2_into_1-expanded"><a name="L318"></a><tt class="py-lineno">318</tt>  <tt class="py-line">    <tt class="py-docstring">"""</tt> </tt>
<a name="L319"></a><tt class="py-lineno">319</tt>  <tt class="py-line"><tt class="py-docstring">    Admix population 2 into population 1.</tt> </tt>
<a name="L320"></a><tt class="py-lineno">320</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L321"></a><tt class="py-lineno">321</tt>  <tt class="py-line"><tt class="py-docstring">    Alters phi in place and returns the new version.</tt> </tt>
<a name="L322"></a><tt class="py-lineno">322</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L323"></a><tt class="py-lineno">323</tt>  <tt class="py-line"><tt class="py-docstring">    phi:   phi corresponding to original 2 populations</tt> </tt>
<a name="L324"></a><tt class="py-lineno">324</tt>  <tt class="py-line"><tt class="py-docstring">    f:     Fraction of updated population 1 to be derived from population 2. </tt> </tt>
<a name="L325"></a><tt class="py-lineno">325</tt>  <tt class="py-line"><tt class="py-docstring">             (A fraction 1-f will be derived from the original population 1.)</tt> </tt>
<a name="L326"></a><tt class="py-lineno">326</tt>  <tt class="py-line"><tt class="py-docstring">    xx,yy: Mapping of points in phi to frequencies in populations 1 and 2.</tt> </tt>
<a name="L327"></a><tt class="py-lineno">327</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="L328"></a><tt class="py-lineno">328</tt>  <tt class="py-line">    <tt class="py-comment"># Note that it's 1-f here since f now denotes the fraction coming from</tt> </tt>
<a name="L329"></a><tt class="py-lineno">329</tt>  <tt class="py-line">    <tt class="py-comment"># population 2.</tt> </tt>
<a name="L330"></a><tt class="py-lineno">330</tt>  <tt class="py-line">    <tt class="py-name">lower_z_index</tt><tt class="py-op">,</tt> <tt class="py-name">upper_z_index</tt><tt class="py-op">,</tt> <tt class="py-name">frac_lower</tt><tt class="py-op">,</tt> <tt class="py-name">frac_upper</tt><tt class="py-op">,</tt> <tt class="py-name">norm</tt> \ </tt>
<a name="L331"></a><tt class="py-lineno">331</tt>  <tt class="py-line">            <tt class="py-op">=</tt> <tt id="link-13" class="py-name"><a title="dadi.PhiManip._two_pop_admixture_intermediates" class="py-name" href="#" onclick="return doclink('link-13', '_two_pop_admixture_intermediates', 'link-9');">_two_pop_admixture_intermediates</a></tt><tt class="py-op">(</tt><tt class="py-name">phi</tt><tt class="py-op">,</tt> <tt class="py-number">1</tt><tt class="py-op">-</tt><tt class="py-name">f</tt><tt class="py-op">,</tt> <tt class="py-name">xx</tt><tt class="py-op">,</tt><tt class="py-name">yy</tt><tt class="py-op">,</tt><tt class="py-name">xx</tt><tt class="py-op">)</tt> </tt>
<a name="L332"></a><tt class="py-lineno">332</tt>  <tt class="py-line"> </tt>
<a name="L333"></a><tt class="py-lineno">333</tt>  <tt class="py-line">    <tt class="py-name">idx_i</tt> <tt class="py-op">=</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">arange</tt><tt class="py-op">(</tt><tt class="py-name">phi</tt><tt class="py-op">.</tt><tt class="py-name">shape</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L334"></a><tt class="py-lineno">334</tt>  <tt class="py-line">    <tt class="py-name">lower_cont</tt> <tt class="py-op">=</tt> <tt class="py-name">frac_lower</tt><tt class="py-op">*</tt><tt class="py-name">norm</tt> </tt>
<a name="L335"></a><tt class="py-lineno">335</tt>  <tt class="py-line">    <tt class="py-name">upper_cont</tt> <tt class="py-op">=</tt> <tt class="py-name">frac_upper</tt><tt class="py-op">*</tt><tt class="py-name">norm</tt> </tt>
<a name="L336"></a><tt class="py-lineno">336</tt>  <tt class="py-line">    <tt class="py-keyword">for</tt> <tt class="py-name">jj</tt> <tt class="py-keyword">in</tt> <tt class="py-name">xrange</tt><tt class="py-op">(</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">yy</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L337"></a><tt class="py-lineno">337</tt>  <tt class="py-line">        <tt class="py-name">phi_int</tt> <tt class="py-op">=</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">zeros</tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">xx</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">xx</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L338"></a><tt class="py-lineno">338</tt>  <tt class="py-line">        <tt class="py-name">phi_int</tt><tt class="py-op">[</tt><tt class="py-name">idx_i</tt><tt class="py-op">,</tt> <tt class="py-name">lower_z_index</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-op">,</tt><tt class="py-name">jj</tt><tt class="py-op">]</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">lower_cont</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-op">,</tt><tt class="py-name">jj</tt><tt class="py-op">]</tt> </tt>
<a name="L339"></a><tt class="py-lineno">339</tt>  <tt class="py-line">        <tt class="py-name">phi_int</tt><tt class="py-op">[</tt><tt class="py-name">idx_i</tt><tt class="py-op">,</tt> <tt class="py-name">upper_z_index</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-op">,</tt><tt class="py-name">jj</tt><tt class="py-op">]</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">upper_cont</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-op">,</tt><tt class="py-name">jj</tt><tt class="py-op">]</tt> </tt>
<a name="L340"></a><tt class="py-lineno">340</tt>  <tt class="py-line">        <tt class="py-name">phi</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-op">,</tt><tt class="py-name">jj</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt id="link-14" class="py-name"><a title="dadi.Numerics" class="py-name" href="#" onclick="return doclink('link-14', 'Numerics', 'link-1');">Numerics</a></tt><tt class="py-op">.</tt><tt id="link-15" class="py-name"><a title="dadi.Numerics.trapz" class="py-name" href="#" onclick="return doclink('link-15', 'trapz', 'link-12');">trapz</a></tt><tt class="py-op">(</tt><tt class="py-name">phi_int</tt><tt class="py-op">,</tt> <tt class="py-name">xx</tt><tt class="py-op">,</tt> <tt class="py-name">axis</tt><tt class="py-op">=</tt><tt class="py-number">0</tt><tt class="py-op">)</tt> </tt>
<a name="L341"></a><tt class="py-lineno">341</tt>  <tt class="py-line"> </tt>
<a name="L342"></a><tt class="py-lineno">342</tt>  <tt class="py-line">    <tt class="py-keyword">return</tt> <tt class="py-name">phi</tt> </tt>
</div><a name="L343"></a><tt class="py-lineno">343</tt>  <tt class="py-line"> </tt>
<a name="phi_3D_admix_1_and_2_into_3"></a><div id="phi_3D_admix_1_and_2_into_3-def"><a name="L344"></a><tt class="py-lineno">344</tt> <a class="py-toggle" href="#" id="phi_3D_admix_1_and_2_into_3-toggle" onclick="return toggle('phi_3D_admix_1_and_2_into_3');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="dadi.PhiManip-module.html#phi_3D_admix_1_and_2_into_3">phi_3D_admix_1_and_2_into_3</a><tt class="py-op">(</tt><tt class="py-param">phi</tt><tt class="py-op">,</tt> <tt class="py-param">f1</tt><tt class="py-op">,</tt><tt class="py-param">f2</tt><tt class="py-op">,</tt> <tt class="py-param">xx</tt><tt class="py-op">,</tt><tt class="py-param">yy</tt><tt class="py-op">,</tt><tt class="py-param">zz</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="phi_3D_admix_1_and_2_into_3-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="phi_3D_admix_1_and_2_into_3-expanded"><a name="L345"></a><tt class="py-lineno">345</tt>  <tt class="py-line">    <tt class="py-docstring">"""</tt> </tt>
<a name="L346"></a><tt class="py-lineno">346</tt>  <tt class="py-line"><tt class="py-docstring">    Admix populations 1 and 2 into population 3.</tt> </tt>
<a name="L347"></a><tt class="py-lineno">347</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L348"></a><tt class="py-lineno">348</tt>  <tt class="py-line"><tt class="py-docstring">    Alters phi in place and returns the new version.</tt> </tt>
<a name="L349"></a><tt class="py-lineno">349</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L350"></a><tt class="py-lineno">350</tt>  <tt class="py-line"><tt class="py-docstring">    phi:      phi corresponding to original 3 populations.</tt> </tt>
<a name="L351"></a><tt class="py-lineno">351</tt>  <tt class="py-line"><tt class="py-docstring">    f1:       Fraction of updated population 3 to be derived from population 1. </tt> </tt>
<a name="L352"></a><tt class="py-lineno">352</tt>  <tt class="py-line"><tt class="py-docstring">    f2:       Fraction of updated population 3 to be derived from population 2. </tt> </tt>
<a name="L353"></a><tt class="py-lineno">353</tt>  <tt class="py-line"><tt class="py-docstring">              A fraction (1-f1-f2) will be derived from the original pop 3.</tt> </tt>
<a name="L354"></a><tt class="py-lineno">354</tt>  <tt class="py-line"><tt class="py-docstring">    xx,yy,zz: Mapping of points in phi to frequencies in populations 1,2 and 3.</tt> </tt>
<a name="L355"></a><tt class="py-lineno">355</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="L356"></a><tt class="py-lineno">356</tt>  <tt class="py-line">    <tt class="py-name">lower_w_index</tt><tt class="py-op">,</tt> <tt class="py-name">upper_w_index</tt><tt class="py-op">,</tt> <tt class="py-name">frac_lower</tt><tt class="py-op">,</tt> <tt class="py-name">frac_upper</tt><tt class="py-op">,</tt> <tt class="py-name">norm</tt> \ </tt>
<a name="L357"></a><tt class="py-lineno">357</tt>  <tt class="py-line">            <tt class="py-op">=</tt> <tt id="link-16" class="py-name" targets="Function dadi.PhiManip._three_pop_admixture_intermediates()=dadi.PhiManip-module.html#_three_pop_admixture_intermediates"><a title="dadi.PhiManip._three_pop_admixture_intermediates" class="py-name" href="#" onclick="return doclink('link-16', '_three_pop_admixture_intermediates', 'link-16');">_three_pop_admixture_intermediates</a></tt><tt class="py-op">(</tt><tt class="py-name">phi</tt><tt class="py-op">,</tt> <tt class="py-name">f1</tt><tt class="py-op">,</tt><tt class="py-name">f2</tt><tt class="py-op">,</tt> <tt class="py-name">xx</tt><tt class="py-op">,</tt><tt class="py-name">yy</tt><tt class="py-op">,</tt><tt class="py-name">zz</tt><tt class="py-op">,</tt> <tt class="py-name">zz</tt><tt class="py-op">)</tt> </tt>
<a name="L358"></a><tt class="py-lineno">358</tt>  <tt class="py-line"> </tt>
<a name="L359"></a><tt class="py-lineno">359</tt>  <tt class="py-line">    <tt class="py-name">lower_cont</tt> <tt class="py-op">=</tt> <tt class="py-name">frac_lower</tt> <tt class="py-op">*</tt> <tt class="py-name">norm</tt> </tt>
<a name="L360"></a><tt class="py-lineno">360</tt>  <tt class="py-line">    <tt class="py-name">upper_cont</tt> <tt class="py-op">=</tt> <tt class="py-name">frac_upper</tt> <tt class="py-op">*</tt> <tt class="py-name">norm</tt> </tt>
<a name="L361"></a><tt class="py-lineno">361</tt>  <tt class="py-line"> </tt>
<a name="L362"></a><tt class="py-lineno">362</tt>  <tt class="py-line">    <tt class="py-comment"># Basically, we're splitting into a fourth ww population, then integrating</tt> </tt>
<a name="L363"></a><tt class="py-lineno">363</tt>  <tt class="py-line">    <tt class="py-comment"># over zz to be left with the two populations we care about.</tt> </tt>
<a name="L364"></a><tt class="py-lineno">364</tt>  <tt class="py-line">    <tt class="py-name">idx_k</tt> <tt class="py-op">=</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">arange</tt><tt class="py-op">(</tt><tt class="py-name">phi</tt><tt class="py-op">.</tt><tt class="py-name">shape</tt><tt class="py-op">[</tt><tt class="py-number">2</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L365"></a><tt class="py-lineno">365</tt>  <tt class="py-line">    <tt class="py-keyword">for</tt> <tt class="py-name">ii</tt> <tt class="py-keyword">in</tt> <tt class="py-name">xrange</tt><tt class="py-op">(</tt><tt class="py-name">phi</tt><tt class="py-op">.</tt><tt class="py-name">shape</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L366"></a><tt class="py-lineno">366</tt>  <tt class="py-line">        <tt class="py-keyword">for</tt> <tt class="py-name">jj</tt> <tt class="py-keyword">in</tt> <tt class="py-name">xrange</tt><tt class="py-op">(</tt><tt class="py-name">phi</tt><tt class="py-op">.</tt><tt class="py-name">shape</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L367"></a><tt class="py-lineno">367</tt>  <tt class="py-line">            <tt class="py-name">phi_int</tt> <tt class="py-op">=</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">zeros</tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-name">phi</tt><tt class="py-op">.</tt><tt class="py-name">shape</tt><tt class="py-op">[</tt><tt class="py-number">2</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">phi</tt><tt class="py-op">.</tt><tt class="py-name">shape</tt><tt class="py-op">[</tt><tt class="py-number">2</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L368"></a><tt class="py-lineno">368</tt>  <tt class="py-line">            <tt class="py-name">phi_int</tt><tt class="py-op">[</tt><tt class="py-name">idx_k</tt><tt class="py-op">,</tt> <tt class="py-name">lower_w_index</tt><tt class="py-op">[</tt><tt class="py-name">ii</tt><tt class="py-op">,</tt><tt class="py-name">jj</tt><tt class="py-op">]</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">lower_cont</tt><tt class="py-op">[</tt><tt class="py-name">ii</tt><tt class="py-op">,</tt><tt class="py-name">jj</tt><tt class="py-op">]</tt> </tt>
<a name="L369"></a><tt class="py-lineno">369</tt>  <tt class="py-line">            <tt class="py-name">phi_int</tt><tt class="py-op">[</tt><tt class="py-name">idx_k</tt><tt class="py-op">,</tt> <tt class="py-name">upper_w_index</tt><tt class="py-op">[</tt><tt class="py-name">ii</tt><tt class="py-op">,</tt><tt class="py-name">jj</tt><tt class="py-op">]</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">upper_cont</tt><tt class="py-op">[</tt><tt class="py-name">ii</tt><tt class="py-op">,</tt><tt class="py-name">jj</tt><tt class="py-op">]</tt> </tt>
<a name="L370"></a><tt class="py-lineno">370</tt>  <tt class="py-line">            <tt class="py-name">phi</tt><tt class="py-op">[</tt><tt class="py-name">ii</tt><tt class="py-op">,</tt><tt class="py-name">jj</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt id="link-17" class="py-name"><a title="dadi.Numerics" class="py-name" href="#" onclick="return doclink('link-17', 'Numerics', 'link-1');">Numerics</a></tt><tt class="py-op">.</tt><tt id="link-18" class="py-name"><a title="dadi.Numerics.trapz" class="py-name" href="#" onclick="return doclink('link-18', 'trapz', 'link-12');">trapz</a></tt><tt class="py-op">(</tt><tt class="py-name">phi_int</tt><tt class="py-op">,</tt> <tt class="py-name">zz</tt><tt class="py-op">,</tt> <tt class="py-name">axis</tt><tt class="py-op">=</tt><tt class="py-number">0</tt><tt class="py-op">)</tt> </tt>
<a name="L371"></a><tt class="py-lineno">371</tt>  <tt class="py-line"> </tt>
<a name="L372"></a><tt class="py-lineno">372</tt>  <tt class="py-line">    <tt class="py-keyword">return</tt> <tt class="py-name">phi</tt> </tt>
</div><a name="L373"></a><tt class="py-lineno">373</tt>  <tt class="py-line"> </tt>
<a name="phi_3D_admix_1_and_3_into_2"></a><div id="phi_3D_admix_1_and_3_into_2-def"><a name="L374"></a><tt class="py-lineno">374</tt> <a class="py-toggle" href="#" id="phi_3D_admix_1_and_3_into_2-toggle" onclick="return toggle('phi_3D_admix_1_and_3_into_2');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="dadi.PhiManip-module.html#phi_3D_admix_1_and_3_into_2">phi_3D_admix_1_and_3_into_2</a><tt class="py-op">(</tt><tt class="py-param">phi</tt><tt class="py-op">,</tt> <tt class="py-param">f1</tt><tt class="py-op">,</tt><tt class="py-param">f3</tt><tt class="py-op">,</tt> <tt class="py-param">xx</tt><tt class="py-op">,</tt><tt class="py-param">yy</tt><tt class="py-op">,</tt><tt class="py-param">zz</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="phi_3D_admix_1_and_3_into_2-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="phi_3D_admix_1_and_3_into_2-expanded"><a name="L375"></a><tt class="py-lineno">375</tt>  <tt class="py-line">    <tt class="py-docstring">"""</tt> </tt>
<a name="L376"></a><tt class="py-lineno">376</tt>  <tt class="py-line"><tt class="py-docstring">    Admix populations 1 and 3 into population 2.</tt> </tt>
<a name="L377"></a><tt class="py-lineno">377</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L378"></a><tt class="py-lineno">378</tt>  <tt class="py-line"><tt class="py-docstring">    Alters phi in place and returns the new version.</tt> </tt>
<a name="L379"></a><tt class="py-lineno">379</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L380"></a><tt class="py-lineno">380</tt>  <tt class="py-line"><tt class="py-docstring">    phi:      phi corresponding to original 3 populations.</tt> </tt>
<a name="L381"></a><tt class="py-lineno">381</tt>  <tt class="py-line"><tt class="py-docstring">    f1:       Fraction of updated population 2 to be derived from population 1. </tt> </tt>
<a name="L382"></a><tt class="py-lineno">382</tt>  <tt class="py-line"><tt class="py-docstring">    f3:       Fraction of updated population 2 to be derived from population 3. </tt> </tt>
<a name="L383"></a><tt class="py-lineno">383</tt>  <tt class="py-line"><tt class="py-docstring">              A fraction (1-f1-f3) will be derived from the original pop 2.</tt> </tt>
<a name="L384"></a><tt class="py-lineno">384</tt>  <tt class="py-line"><tt class="py-docstring">    xx,yy,zz: Mapping of points in phi to frequencies in populations 1,2 and 3.</tt> </tt>
<a name="L385"></a><tt class="py-lineno">385</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="L386"></a><tt class="py-lineno">386</tt>  <tt class="py-line">    <tt class="py-name">lower_w_index</tt><tt class="py-op">,</tt> <tt class="py-name">upper_w_index</tt><tt class="py-op">,</tt> <tt class="py-name">frac_lower</tt><tt class="py-op">,</tt> <tt class="py-name">frac_upper</tt><tt class="py-op">,</tt> <tt class="py-name">norm</tt> \ </tt>
<a name="L387"></a><tt class="py-lineno">387</tt>  <tt class="py-line">            <tt class="py-op">=</tt> <tt id="link-19" class="py-name"><a title="dadi.PhiManip._three_pop_admixture_intermediates" class="py-name" href="#" onclick="return doclink('link-19', '_three_pop_admixture_intermediates', 'link-16');">_three_pop_admixture_intermediates</a></tt><tt class="py-op">(</tt><tt class="py-name">phi</tt><tt class="py-op">,</tt> <tt class="py-name">f1</tt><tt class="py-op">,</tt><tt class="py-number">1</tt><tt class="py-op">-</tt><tt class="py-name">f1</tt><tt class="py-op">-</tt><tt class="py-name">f3</tt><tt class="py-op">,</tt> <tt class="py-name">xx</tt><tt class="py-op">,</tt><tt class="py-name">yy</tt><tt class="py-op">,</tt><tt class="py-name">zz</tt><tt class="py-op">,</tt> <tt class="py-name">yy</tt><tt class="py-op">)</tt> </tt>
<a name="L388"></a><tt class="py-lineno">388</tt>  <tt class="py-line"> </tt>
<a name="L389"></a><tt class="py-lineno">389</tt>  <tt class="py-line">    <tt class="py-name">lower_cont</tt> <tt class="py-op">=</tt> <tt class="py-name">frac_lower</tt> <tt class="py-op">*</tt> <tt class="py-name">norm</tt> </tt>
<a name="L390"></a><tt class="py-lineno">390</tt>  <tt class="py-line">    <tt class="py-name">upper_cont</tt> <tt class="py-op">=</tt> <tt class="py-name">frac_upper</tt> <tt class="py-op">*</tt> <tt class="py-name">norm</tt> </tt>
<a name="L391"></a><tt class="py-lineno">391</tt>  <tt class="py-line"> </tt>
<a name="L392"></a><tt class="py-lineno">392</tt>  <tt class="py-line">    <tt class="py-comment"># Basically, we're splitting into a fourth ww population, then integrating</tt> </tt>
<a name="L393"></a><tt class="py-lineno">393</tt>  <tt class="py-line">    <tt class="py-comment"># over yy to be left with the two populations we care about.</tt> </tt>
<a name="L394"></a><tt class="py-lineno">394</tt>  <tt class="py-line">    <tt class="py-name">idx_j</tt> <tt class="py-op">=</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">arange</tt><tt class="py-op">(</tt><tt class="py-name">phi</tt><tt class="py-op">.</tt><tt class="py-name">shape</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L395"></a><tt class="py-lineno">395</tt>  <tt class="py-line">    <tt class="py-keyword">for</tt> <tt class="py-name">ii</tt> <tt class="py-keyword">in</tt> <tt class="py-name">xrange</tt><tt class="py-op">(</tt><tt class="py-name">phi</tt><tt class="py-op">.</tt><tt class="py-name">shape</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L396"></a><tt class="py-lineno">396</tt>  <tt class="py-line">        <tt class="py-keyword">for</tt> <tt class="py-name">kk</tt> <tt class="py-keyword">in</tt> <tt class="py-name">xrange</tt><tt class="py-op">(</tt><tt class="py-name">phi</tt><tt class="py-op">.</tt><tt class="py-name">shape</tt><tt class="py-op">[</tt><tt class="py-number">2</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L397"></a><tt class="py-lineno">397</tt>  <tt class="py-line">            <tt class="py-name">phi_int</tt> <tt class="py-op">=</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">zeros</tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-name">phi</tt><tt class="py-op">.</tt><tt class="py-name">shape</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">phi</tt><tt class="py-op">.</tt><tt class="py-name">shape</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L398"></a><tt class="py-lineno">398</tt>  <tt class="py-line">            <tt class="py-name">phi_int</tt><tt class="py-op">[</tt><tt class="py-name">idx_j</tt><tt class="py-op">,</tt> <tt class="py-name">lower_w_index</tt><tt class="py-op">[</tt><tt class="py-name">ii</tt><tt class="py-op">,</tt><tt class="py-op">:</tt><tt class="py-op">,</tt><tt class="py-name">kk</tt><tt class="py-op">]</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">lower_cont</tt><tt class="py-op">[</tt><tt class="py-name">ii</tt><tt class="py-op">,</tt><tt class="py-op">:</tt><tt class="py-op">,</tt><tt class="py-name">kk</tt><tt class="py-op">]</tt> </tt>
<a name="L399"></a><tt class="py-lineno">399</tt>  <tt class="py-line">            <tt class="py-name">phi_int</tt><tt class="py-op">[</tt><tt class="py-name">idx_j</tt><tt class="py-op">,</tt> <tt class="py-name">upper_w_index</tt><tt class="py-op">[</tt><tt class="py-name">ii</tt><tt class="py-op">,</tt><tt class="py-op">:</tt><tt class="py-op">,</tt><tt class="py-name">kk</tt><tt class="py-op">]</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">upper_cont</tt><tt class="py-op">[</tt><tt class="py-name">ii</tt><tt class="py-op">,</tt><tt class="py-op">:</tt><tt class="py-op">,</tt><tt class="py-name">kk</tt><tt class="py-op">]</tt> </tt>
<a name="L400"></a><tt class="py-lineno">400</tt>  <tt class="py-line">            <tt class="py-name">phi</tt><tt class="py-op">[</tt><tt class="py-name">ii</tt><tt class="py-op">,</tt><tt class="py-op">:</tt><tt class="py-op">,</tt><tt class="py-name">kk</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt id="link-20" class="py-name"><a title="dadi.Numerics" class="py-name" href="#" onclick="return doclink('link-20', 'Numerics', 'link-1');">Numerics</a></tt><tt class="py-op">.</tt><tt id="link-21" class="py-name"><a title="dadi.Numerics.trapz" class="py-name" href="#" onclick="return doclink('link-21', 'trapz', 'link-12');">trapz</a></tt><tt class="py-op">(</tt><tt class="py-name">phi_int</tt><tt class="py-op">,</tt> <tt class="py-name">yy</tt><tt class="py-op">,</tt> <tt class="py-name">axis</tt><tt class="py-op">=</tt><tt class="py-number">0</tt><tt class="py-op">)</tt> </tt>
<a name="L401"></a><tt class="py-lineno">401</tt>  <tt class="py-line"> </tt>
<a name="L402"></a><tt class="py-lineno">402</tt>  <tt class="py-line">    <tt class="py-keyword">return</tt> <tt class="py-name">phi</tt> </tt>
</div><a name="L403"></a><tt class="py-lineno">403</tt>  <tt class="py-line"> </tt>
<a name="phi_3D_admix_2_and_3_into_1"></a><div id="phi_3D_admix_2_and_3_into_1-def"><a name="L404"></a><tt class="py-lineno">404</tt> <a class="py-toggle" href="#" id="phi_3D_admix_2_and_3_into_1-toggle" onclick="return toggle('phi_3D_admix_2_and_3_into_1');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="dadi.PhiManip-module.html#phi_3D_admix_2_and_3_into_1">phi_3D_admix_2_and_3_into_1</a><tt class="py-op">(</tt><tt class="py-param">phi</tt><tt class="py-op">,</tt> <tt class="py-param">f2</tt><tt class="py-op">,</tt><tt class="py-param">f3</tt><tt class="py-op">,</tt> <tt class="py-param">xx</tt><tt class="py-op">,</tt><tt class="py-param">yy</tt><tt class="py-op">,</tt><tt class="py-param">zz</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="phi_3D_admix_2_and_3_into_1-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="phi_3D_admix_2_and_3_into_1-expanded"><a name="L405"></a><tt class="py-lineno">405</tt>  <tt class="py-line">    <tt class="py-docstring">"""</tt> </tt>
<a name="L406"></a><tt class="py-lineno">406</tt>  <tt class="py-line"><tt class="py-docstring">    Admix populations 2 and 3 into population 1.</tt> </tt>
<a name="L407"></a><tt class="py-lineno">407</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L408"></a><tt class="py-lineno">408</tt>  <tt class="py-line"><tt class="py-docstring">    Alters phi in place and returns the new version.</tt> </tt>
<a name="L409"></a><tt class="py-lineno">409</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L410"></a><tt class="py-lineno">410</tt>  <tt class="py-line"><tt class="py-docstring">    phi:      phi corresponding to original 3 populations.</tt> </tt>
<a name="L411"></a><tt class="py-lineno">411</tt>  <tt class="py-line"><tt class="py-docstring">    f2:       Fraction of updated population 1 to be derived from population 2. </tt> </tt>
<a name="L412"></a><tt class="py-lineno">412</tt>  <tt class="py-line"><tt class="py-docstring">    f3:       Fraction of updated population 1 to be derived from population 3. </tt> </tt>
<a name="L413"></a><tt class="py-lineno">413</tt>  <tt class="py-line"><tt class="py-docstring">              A fraction (1-f2-f3) will be derived from the original pop 1.</tt> </tt>
<a name="L414"></a><tt class="py-lineno">414</tt>  <tt class="py-line"><tt class="py-docstring">    xx,yy,zz: Mapping of points in phi to frequencies in populations 1,2 and 3.</tt> </tt>
<a name="L415"></a><tt class="py-lineno">415</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="L416"></a><tt class="py-lineno">416</tt>  <tt class="py-line">    <tt class="py-name">lower_w_index</tt><tt class="py-op">,</tt> <tt class="py-name">upper_w_index</tt><tt class="py-op">,</tt> <tt class="py-name">frac_lower</tt><tt class="py-op">,</tt> <tt class="py-name">frac_upper</tt><tt class="py-op">,</tt> <tt class="py-name">norm</tt> \ </tt>
<a name="L417"></a><tt class="py-lineno">417</tt>  <tt class="py-line">            <tt class="py-op">=</tt> <tt id="link-22" class="py-name"><a title="dadi.PhiManip._three_pop_admixture_intermediates" class="py-name" href="#" onclick="return doclink('link-22', '_three_pop_admixture_intermediates', 'link-16');">_three_pop_admixture_intermediates</a></tt><tt class="py-op">(</tt><tt class="py-name">phi</tt><tt class="py-op">,</tt> <tt class="py-number">1</tt><tt class="py-op">-</tt><tt class="py-name">f2</tt><tt class="py-op">-</tt><tt class="py-name">f3</tt><tt class="py-op">,</tt><tt class="py-name">f2</tt><tt class="py-op">,</tt> <tt class="py-name">xx</tt><tt class="py-op">,</tt><tt class="py-name">yy</tt><tt class="py-op">,</tt><tt class="py-name">zz</tt><tt class="py-op">,</tt> <tt class="py-name">xx</tt><tt class="py-op">)</tt> </tt>
<a name="L418"></a><tt class="py-lineno">418</tt>  <tt class="py-line"> </tt>
<a name="L419"></a><tt class="py-lineno">419</tt>  <tt class="py-line">    <tt class="py-name">lower_cont</tt> <tt class="py-op">=</tt> <tt class="py-name">frac_lower</tt> <tt class="py-op">*</tt> <tt class="py-name">norm</tt> </tt>
<a name="L420"></a><tt class="py-lineno">420</tt>  <tt class="py-line">    <tt class="py-name">upper_cont</tt> <tt class="py-op">=</tt> <tt class="py-name">frac_upper</tt> <tt class="py-op">*</tt> <tt class="py-name">norm</tt> </tt>
<a name="L421"></a><tt class="py-lineno">421</tt>  <tt class="py-line"> </tt>
<a name="L422"></a><tt class="py-lineno">422</tt>  <tt class="py-line">    <tt class="py-comment"># Basically, we're splitting into a fourth ww population, then integrating</tt> </tt>
<a name="L423"></a><tt class="py-lineno">423</tt>  <tt class="py-line">    <tt class="py-comment"># over yy to be left with the two populations we care about.</tt> </tt>
<a name="L424"></a><tt class="py-lineno">424</tt>  <tt class="py-line">    <tt class="py-name">idx_i</tt> <tt class="py-op">=</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">arange</tt><tt class="py-op">(</tt><tt class="py-name">phi</tt><tt class="py-op">.</tt><tt class="py-name">shape</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L425"></a><tt class="py-lineno">425</tt>  <tt class="py-line">    <tt class="py-keyword">for</tt> <tt class="py-name">jj</tt> <tt class="py-keyword">in</tt> <tt class="py-name">xrange</tt><tt class="py-op">(</tt><tt class="py-name">phi</tt><tt class="py-op">.</tt><tt class="py-name">shape</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L426"></a><tt class="py-lineno">426</tt>  <tt class="py-line">        <tt class="py-keyword">for</tt> <tt class="py-name">kk</tt> <tt class="py-keyword">in</tt> <tt class="py-name">xrange</tt><tt class="py-op">(</tt><tt class="py-name">phi</tt><tt class="py-op">.</tt><tt class="py-name">shape</tt><tt class="py-op">[</tt><tt class="py-number">2</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L427"></a><tt class="py-lineno">427</tt>  <tt class="py-line">            <tt class="py-name">phi_int</tt> <tt class="py-op">=</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">zeros</tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-name">phi</tt><tt class="py-op">.</tt><tt class="py-name">shape</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">phi</tt><tt class="py-op">.</tt><tt class="py-name">shape</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L428"></a><tt class="py-lineno">428</tt>  <tt class="py-line">            <tt class="py-name">phi_int</tt><tt class="py-op">[</tt><tt class="py-name">idx_i</tt><tt class="py-op">,</tt> <tt class="py-name">lower_w_index</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-op">,</tt><tt class="py-name">jj</tt><tt class="py-op">,</tt><tt class="py-name">kk</tt><tt class="py-op">]</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">lower_cont</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-op">,</tt><tt class="py-name">jj</tt><tt class="py-op">,</tt><tt class="py-name">kk</tt><tt class="py-op">]</tt> </tt>
<a name="L429"></a><tt class="py-lineno">429</tt>  <tt class="py-line">            <tt class="py-name">phi_int</tt><tt class="py-op">[</tt><tt class="py-name">idx_i</tt><tt class="py-op">,</tt> <tt class="py-name">upper_w_index</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-op">,</tt><tt class="py-name">jj</tt><tt class="py-op">,</tt><tt class="py-name">kk</tt><tt class="py-op">]</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">upper_cont</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-op">,</tt><tt class="py-name">jj</tt><tt class="py-op">,</tt><tt class="py-name">kk</tt><tt class="py-op">]</tt> </tt>
<a name="L430"></a><tt class="py-lineno">430</tt>  <tt class="py-line">            <tt class="py-name">phi</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-op">,</tt><tt class="py-name">jj</tt><tt class="py-op">,</tt><tt class="py-name">kk</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt id="link-23" class="py-name"><a title="dadi.Numerics" class="py-name" href="#" onclick="return doclink('link-23', 'Numerics', 'link-1');">Numerics</a></tt><tt class="py-op">.</tt><tt id="link-24" class="py-name"><a title="dadi.Numerics.trapz" class="py-name" href="#" onclick="return doclink('link-24', 'trapz', 'link-12');">trapz</a></tt><tt class="py-op">(</tt><tt class="py-name">phi_int</tt><tt class="py-op">,</tt> <tt class="py-name">xx</tt><tt class="py-op">,</tt> <tt class="py-name">axis</tt><tt class="py-op">=</tt><tt class="py-number">0</tt><tt class="py-op">)</tt> </tt>
<a name="L431"></a><tt class="py-lineno">431</tt>  <tt class="py-line"> </tt>
<a name="L432"></a><tt class="py-lineno">432</tt>  <tt class="py-line">    <tt class="py-keyword">return</tt> <tt class="py-name">phi</tt> </tt>
</div><a name="L433"></a><tt class="py-lineno">433</tt>  <tt class="py-line"> </tt>
<a name="remove_pop"></a><div id="remove_pop-def"><a name="L434"></a><tt class="py-lineno">434</tt> <a class="py-toggle" href="#" id="remove_pop-toggle" onclick="return toggle('remove_pop');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="dadi.PhiManip-module.html#remove_pop">remove_pop</a><tt class="py-op">(</tt><tt class="py-param">phi</tt><tt class="py-op">,</tt> <tt class="py-param">xx</tt><tt class="py-op">,</tt> <tt class="py-param">popnum</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="remove_pop-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="remove_pop-expanded"><a name="L435"></a><tt class="py-lineno">435</tt>  <tt class="py-line">    <tt class="py-docstring">"""</tt> </tt>
<a name="L436"></a><tt class="py-lineno">436</tt>  <tt class="py-line"><tt class="py-docstring">    Remove a population from phi.</tt> </tt>
<a name="L437"></a><tt class="py-lineno">437</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L438"></a><tt class="py-lineno">438</tt>  <tt class="py-line"><tt class="py-docstring">    Returns new phi with one fewer population.</tt> </tt>
<a name="L439"></a><tt class="py-lineno">439</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L440"></a><tt class="py-lineno">440</tt>  <tt class="py-line"><tt class="py-docstring">    phi: phi corresponding to original populations</tt> </tt>
<a name="L441"></a><tt class="py-lineno">441</tt>  <tt class="py-line"><tt class="py-docstring">    xx: Mapping of points in phi to frequencies in population to be removed</tt> </tt>
<a name="L442"></a><tt class="py-lineno">442</tt>  <tt class="py-line"><tt class="py-docstring">    popnum: Population number to remove, numbering from 1.</tt> </tt>
<a name="L443"></a><tt class="py-lineno">443</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="L444"></a><tt class="py-lineno">444</tt>  <tt class="py-line">    <tt class="py-keyword">return</tt> <tt id="link-25" class="py-name"><a title="dadi.Numerics" class="py-name" href="#" onclick="return doclink('link-25', 'Numerics', 'link-1');">Numerics</a></tt><tt class="py-op">.</tt><tt id="link-26" class="py-name"><a title="dadi.Numerics.trapz" class="py-name" href="#" onclick="return doclink('link-26', 'trapz', 'link-12');">trapz</a></tt><tt class="py-op">(</tt><tt class="py-name">phi</tt><tt class="py-op">,</tt> <tt class="py-name">xx</tt><tt class="py-op">,</tt> <tt class="py-name">axis</tt><tt class="py-op">=</tt><tt class="py-name">popnum</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
</div><a name="L445"></a><tt class="py-lineno">445</tt>  <tt class="py-line"> </tt>
<a name="phi_1D_X"></a><div id="phi_1D_X-def"><a name="L446"></a><tt class="py-lineno">446</tt> <a class="py-toggle" href="#" id="phi_1D_X-toggle" onclick="return toggle('phi_1D_X');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="dadi.PhiManip-module.html#phi_1D_X">phi_1D_X</a><tt class="py-op">(</tt><tt class="py-param">xx</tt><tt class="py-op">,</tt> <tt class="py-param">nu</tt><tt class="py-op">=</tt><tt class="py-number">1.0</tt><tt class="py-op">,</tt> <tt class="py-param">theta0</tt><tt class="py-op">=</tt><tt class="py-number">1.0</tt><tt class="py-op">,</tt> <tt class="py-param">gamma</tt><tt class="py-op">=</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-param">h</tt><tt class="py-op">=</tt><tt class="py-number">0.5</tt><tt class="py-op">,</tt> <tt class="py-param">beta</tt><tt class="py-op">=</tt><tt class="py-number">1</tt><tt class="py-op">,</tt> <tt class="py-param">alpha</tt><tt class="py-op">=</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="phi_1D_X-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="phi_1D_X-expanded"><a name="L447"></a><tt class="py-lineno">447</tt>  <tt class="py-line">    <tt class="py-docstring">"""</tt> </tt>
<a name="L448"></a><tt class="py-lineno">448</tt>  <tt class="py-line"><tt class="py-docstring">    One-dimensional phi for a constant-sized population with genic selection.</tt> </tt>
<a name="L449"></a><tt class="py-lineno">449</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L450"></a><tt class="py-lineno">450</tt>  <tt class="py-line"><tt class="py-docstring">    xx: one-dimensional grid of frequencies upon which phi is defined</tt> </tt>
<a name="L451"></a><tt class="py-lineno">451</tt>  <tt class="py-line"><tt class="py-docstring">    nu: size of this population, relative to the reference population size Nref.</tt> </tt>
<a name="L452"></a><tt class="py-lineno">452</tt>  <tt class="py-line"><tt class="py-docstring">    theta0: scaled mutation rate, equal to 4*Nref * u, where u is the mutation </tt> </tt>
<a name="L453"></a><tt class="py-lineno">453</tt>  <tt class="py-line"><tt class="py-docstring">            event rate per generation for the simulated locus and Nref is the </tt> </tt>
<a name="L454"></a><tt class="py-lineno">454</tt>  <tt class="py-line"><tt class="py-docstring">            reference population size.</tt> </tt>
<a name="L455"></a><tt class="py-lineno">455</tt>  <tt class="py-line"><tt class="py-docstring">    gamma: scaled selection coefficient, equal to 4*Nref * s, where s is the</tt> </tt>
<a name="L456"></a><tt class="py-lineno">456</tt>  <tt class="py-line"><tt class="py-docstring">           selective advantage.</tt> </tt>
<a name="L457"></a><tt class="py-lineno">457</tt>  <tt class="py-line"><tt class="py-docstring">    h: Dominance coefficient. If A is the selected allele, the aa has fitness 1,</tt> </tt>
<a name="L458"></a><tt class="py-lineno">458</tt>  <tt class="py-line"><tt class="py-docstring">       aA has fitness 1+2sh and AA has fitness 1+2s. Male carriers have fitness</tt> </tt>
<a name="L459"></a><tt class="py-lineno">459</tt>  <tt class="py-line"><tt class="py-docstring">       1+2s. h = 0.5 corresonds to genic selection.</tt> </tt>
<a name="L460"></a><tt class="py-lineno">460</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L461"></a><tt class="py-lineno">461</tt>  <tt class="py-line"><tt class="py-docstring">    Returns a new phi array.</tt> </tt>
<a name="L462"></a><tt class="py-lineno">462</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="L463"></a><tt class="py-lineno">463</tt>  <tt class="py-line">    <tt class="py-name">Kv</tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt class="py-number">2.</tt><tt class="py-op">*</tt><tt class="py-name">beta</tt><tt class="py-op">+</tt><tt class="py-number">4.</tt><tt class="py-op">)</tt><tt class="py-op">*</tt><tt class="py-op">(</tt><tt class="py-name">beta</tt><tt class="py-op">+</tt><tt class="py-number">1.</tt><tt class="py-op">)</tt><tt class="py-op">/</tt><tt class="py-op">(</tt><tt class="py-number">9.</tt><tt class="py-op">*</tt><tt class="py-name">beta</tt><tt class="py-op">)</tt> </tt>
<a name="L464"></a><tt class="py-lineno">464</tt>  <tt class="py-line">    <tt class="py-name">Km1</tt> <tt class="py-op">=</tt> <tt class="py-number">4.</tt><tt class="py-op">/</tt><tt class="py-number">3.</tt> <tt class="py-op">*</tt> <tt class="py-name">gamma</tt><tt class="py-op">*</tt><tt class="py-op">(</tt><tt class="py-number">0.5</tt><tt class="py-op">+</tt><tt class="py-name">h</tt><tt class="py-op">)</tt> </tt>
<a name="L465"></a><tt class="py-lineno">465</tt>  <tt class="py-line">    <tt class="py-name">Km2</tt> <tt class="py-op">=</tt> <tt class="py-number">4.</tt><tt class="py-op">/</tt><tt class="py-number">3.</tt><tt class="py-op">*</tt><tt class="py-name">gamma</tt><tt class="py-op">*</tt><tt class="py-op">(</tt><tt class="py-number">1.</tt><tt class="py-op">-</tt><tt class="py-number">2.</tt><tt class="py-op">*</tt><tt class="py-name">h</tt><tt class="py-op">)</tt> </tt>
<a name="L466"></a><tt class="py-lineno">466</tt>  <tt class="py-line">    <tt class="py-name">g1</tt> <tt class="py-op">=</tt> <tt class="py-name">Km1</tt><tt class="py-op">/</tt><tt class="py-name">Kv</tt> </tt>
<a name="L467"></a><tt class="py-lineno">467</tt>  <tt class="py-line">    <tt class="py-name">g2</tt> <tt class="py-op">=</tt> <tt class="py-name">Km2</tt><tt class="py-op">/</tt><tt class="py-name">Kv</tt> </tt>
<a name="L468"></a><tt class="py-lineno">468</tt>  <tt class="py-line"> </tt>
<a name="L469"></a><tt class="py-lineno">469</tt>  <tt class="py-line">    <tt class="py-comment"># First we evaluate the relevant integrals.</tt> </tt>
<a name="L470"></a><tt class="py-lineno">470</tt>  <tt class="py-line">    <tt class="py-name">ints</tt> <tt class="py-op">=</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">empty</tt><tt class="py-op">(</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">xx</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L471"></a><tt class="py-lineno">471</tt>  <tt class="py-line">    <tt class="py-name">integrand</tt> <tt class="py-op">=</tt> <tt class="py-keyword">lambda</tt> <tt class="py-name">xi</tt><tt class="py-op">:</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">exp</tt><tt class="py-op">(</tt><tt class="py-op">-</tt><tt class="py-number">2</tt><tt class="py-op">*</tt><tt class="py-name">g1</tt><tt class="py-op">*</tt><tt class="py-name">xi</tt> <tt class="py-op">-</tt> <tt class="py-name">g2</tt><tt class="py-op">*</tt><tt class="py-name">xi</tt><tt class="py-op">**</tt><tt class="py-number">2</tt><tt class="py-op">)</tt> </tt>
<a name="L472"></a><tt class="py-lineno">472</tt>  <tt class="py-line">    <tt class="py-name">val</tt><tt class="py-op">,</tt> <tt class="py-name">eps</tt> <tt class="py-op">=</tt> <tt class="py-name">scipy</tt><tt class="py-op">.</tt><tt class="py-name">integrate</tt><tt class="py-op">.</tt><tt class="py-name">quad</tt><tt class="py-op">(</tt><tt class="py-name">integrand</tt><tt class="py-op">,</tt> <tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L473"></a><tt class="py-lineno">473</tt>  <tt class="py-line">    <tt class="py-name">int0</tt> <tt class="py-op">=</tt> <tt class="py-name">val</tt> </tt>
<a name="L474"></a><tt class="py-lineno">474</tt>  <tt class="py-line">    <tt class="py-keyword">for</tt> <tt class="py-name">ii</tt><tt class="py-op">,</tt><tt class="py-name">q</tt> <tt class="py-keyword">in</tt> <tt class="py-name">enumerate</tt><tt class="py-op">(</tt><tt class="py-name">xx</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L475"></a><tt class="py-lineno">475</tt>  <tt class="py-line">        <tt class="py-name">val</tt><tt class="py-op">,</tt> <tt class="py-name">eps</tt> <tt class="py-op">=</tt> <tt class="py-name">scipy</tt><tt class="py-op">.</tt><tt class="py-name">integrate</tt><tt class="py-op">.</tt><tt class="py-name">quad</tt><tt class="py-op">(</tt><tt class="py-name">integrand</tt><tt class="py-op">,</tt> <tt class="py-name">q</tt><tt class="py-op">,</tt> <tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L476"></a><tt class="py-lineno">476</tt>  <tt class="py-line">        <tt class="py-name">ints</tt><tt class="py-op">[</tt><tt class="py-name">ii</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">val</tt> </tt>
<a name="L477"></a><tt class="py-lineno">477</tt>  <tt class="py-line"> </tt>
<a name="L478"></a><tt class="py-lineno">478</tt>  <tt class="py-line">    <tt class="py-name">phi</tt> <tt class="py-op">=</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">exp</tt><tt class="py-op">(</tt><tt class="py-number">2</tt><tt class="py-op">*</tt><tt class="py-name">g1</tt><tt class="py-op">*</tt><tt class="py-name">xx</tt> <tt class="py-op">+</tt> <tt class="py-name">g2</tt><tt class="py-op">*</tt><tt class="py-name">xx</tt><tt class="py-op">**</tt><tt class="py-number">2</tt><tt class="py-op">)</tt><tt class="py-op">*</tt><tt class="py-name">ints</tt><tt class="py-op">/</tt><tt class="py-name">int0</tt> </tt>
<a name="L479"></a><tt class="py-lineno">479</tt>  <tt class="py-line">    <tt class="py-comment"># Protect from division by zero errors</tt> </tt>
<a name="L480"></a><tt class="py-lineno">480</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-name">xx</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> <tt class="py-op">==</tt> <tt class="py-number">0</tt> <tt class="py-keyword">and</tt> <tt class="py-name">xx</tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> <tt class="py-op">==</tt> <tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L481"></a><tt class="py-lineno">481</tt>  <tt class="py-line">        <tt class="py-name">phi</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">:</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> <tt class="py-op">*=</tt> <tt class="py-number">1.</tt><tt class="py-op">/</tt><tt class="py-op">(</tt><tt class="py-name">xx</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">:</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">*</tt><tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">-</tt><tt class="py-name">xx</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">:</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L482"></a><tt class="py-lineno">482</tt>  <tt class="py-line">    <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L483"></a><tt class="py-lineno">483</tt>  <tt class="py-line">        <tt class="py-name">phi</tt> <tt class="py-op">*=</tt> <tt class="py-number">1.</tt><tt class="py-op">/</tt><tt class="py-op">(</tt><tt class="py-name">xx</tt><tt class="py-op">*</tt><tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">-</tt><tt class="py-name">xx</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L484"></a><tt class="py-lineno">484</tt>  <tt class="py-line"> </tt>
<a name="L485"></a><tt class="py-lineno">485</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-name">xx</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> <tt class="py-op">==</tt> <tt class="py-number">0</tt><tt class="py-op">:</tt> </tt>
<a name="L486"></a><tt class="py-lineno">486</tt>  <tt class="py-line">        <tt class="py-comment"># Technically, phi diverges at 0. This fixes lets us do numerics</tt> </tt>
<a name="L487"></a><tt class="py-lineno">487</tt>  <tt class="py-line">        <tt class="py-comment"># sensibly.</tt> </tt>
<a name="L488"></a><tt class="py-lineno">488</tt>  <tt class="py-line">        <tt class="py-name">phi</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">phi</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
<a name="L489"></a><tt class="py-lineno">489</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-name">xx</tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> <tt class="py-op">==</tt> <tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L490"></a><tt class="py-lineno">490</tt>  <tt class="py-line">        <tt class="py-comment"># I used Mathematica to check that this was the proper limit.</tt> </tt>
<a name="L491"></a><tt class="py-lineno">491</tt>  <tt class="py-line">        <tt class="py-name">phi</tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-number">1.</tt><tt class="py-op">/</tt><tt class="py-name">int0</tt> </tt>
<a name="L492"></a><tt class="py-lineno">492</tt>  <tt class="py-line">    <tt class="py-keyword">return</tt> <tt class="py-name">phi</tt> <tt class="py-op">*</tt> <tt class="py-name">nu</tt><tt class="py-op">*</tt><tt class="py-name">theta0</tt> <tt class="py-op">*</tt> <tt class="py-number">1.</tt><tt class="py-op">/</tt><tt class="py-name">Kv</tt> <tt class="py-op">*</tt> <tt class="py-number">2.</tt><tt class="py-op">/</tt><tt class="py-op">(</tt><tt class="py-number">1.</tt><tt class="py-op">+</tt><tt class="py-number">2.</tt><tt class="py-op">*</tt><tt class="py-name">beta</tt><tt class="py-op">)</tt><tt class="py-op">*</tt><tt class="py-op">(</tt><tt class="py-number">1.</tt><tt class="py-op">/</tt><tt class="py-op">(</tt><tt class="py-number">1.</tt><tt class="py-op">+</tt><tt class="py-name">alpha</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt class="py-name">beta</tt><tt class="py-op">)</tt> </tt>
</div><a name="L493"></a><tt class="py-lineno">493</tt>  <tt class="py-line"> </tt><script type="text/javascript">
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